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[BUG] created profile does not include a table named `mean_coverage_Q2Q3_splits` ,about merenlab/anvio

Comments (5)

meren commented on July 26, 2024

Hi @NebulaSL,

This is interesting. But the problem you run into, i.e., "profile.db does not have a table named mean_coverage_Q2Q3_splits", is not related to --min-mean-coverage or --min-coverage-for-variability flags. I wish you had not gone that direction :)

The best practice for refining external binning results is to create a single contigs-db using all contigs, and then profile your metagenomes, and import your final collection into the final merged profile database. But that is another topic.

The only reason I can think of why a profile database will be missing a mean_coverage_Q2Q3_splits table is the following: something went wrong and your process was killed prematurely. If the last message you see in your log is the following,

====================================================
According to the data generated in the contigs database, there are 2117978
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_922990_length_375_cov_1.446309"

it means the profiling task certainly did not finish. You should this line at the end of the log for a successful profiling run:

* Happy 😇

Indeed, this is what I see when I run the following command on your profile-db:

sqlite3 PROFILE.db '.tables'
collections_bins_info   item_additional_data    states
collections_info        item_orders             variable_codons
collections_of_contigs  layer_additional_data   variable_nucleotides
collections_of_splits   layer_orders            views
indels                  self

In contrast to this output, which is coming from a profile-db that is successfully finished:

sqlite3 PROFILE.db '.tables'
abundance_contigs           mean_coverage_Q2Q3_splits
abundance_splits            mean_coverage_contigs
collections_bins_info       mean_coverage_splits
collections_info            metabolite_abundances
collections_of_contigs      protein_abundances
collections_of_splits       self
detection_contigs           states
detection_splits            std_coverage_contigs
indels                      std_coverage_splits
item_additional_data        variability_contigs
item_orders                 variability_splits
layer_additional_data       variable_codons
layer_orders                variable_nucleotides
mean_coverage_Q2Q3_contigs  views

Please re-create your profile db (without using --min-mean-coverage, --min-coverage-for-variability, or --report-variability-full unless you have other reasons to believe that you need them), and see if there are any server side / HPC problems.

Best wishes,
Meren

from anvio.

NebulaSL commented on July 26, 2024

Hello @meren!

Thanks for your response!

I tried to run without using --min-mean-coverage, --min-coverage-for-variability, or --report-variability-full, however I still get the following error while creating the profile.

Could this be related to that in the fasta file some. exist when creating contig.db? like >NODE_375_length_48937_cov_8.432583

Regarding to the best practice for external bin refinement you metioned. Are you saying that it woule be better if I use the assembly contig before binning to create the contig.db and then create its profile.db? Or concatenate all my already binned MAGs into one fasta file and then create the contig.gb then create its profile.db?

Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.109_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.109.db
Contigs DB hash ...................................: hash50d729e3
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.109.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.109_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.109_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2117897
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1800471_length_249_cov_0.639535"


✖ anvi-profile encountered an error after 0:00:08.146008


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_21375_length_3530_cov_4.782508'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.112_sub_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.112_sub.db
Contigs DB hash ...................................: hash0f00c5ed
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.112_sub.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.112_sub_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.112_sub_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2117527
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_293983_length_785_cov_1.672316"


✖ anvi-profile encountered an error after 0:00:07.469866


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_20275_length_3642_cov_5.082188'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.116_sub_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.116_sub.db
Contigs DB hash ...................................: hash4afa0e05
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.116_sub.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.116_sub_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.116_sub_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118551
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_802406_length_416_cov_4.171091"


✖ anvi-profile encountered an error after 0:00:07.465892


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_16881_length_4066_cov_4.377288'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.136_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.136.db
Contigs DB hash ...................................: hashd23fedb6
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.136.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.136_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.136_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118383
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1998841_length_235_cov_1.873418"


✖ anvi-profile encountered an error after 0:00:07.590958


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_57280_length_2015_cov_5.567595'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.153_sub_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.153_sub.db
Contigs DB hash ...................................: hashe5a7a44d
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.153_sub.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.153_sub_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.153_sub_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118237
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1679863_length_258_cov_1.226519"


✖ anvi-profile encountered an error after 0:00:07.466719


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_1653_length_20185_cov_12.640889'. You may be using
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.154_sub_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.154_sub.db
Contigs DB hash ...................................: hashc18e1733
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.154_sub.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.154_sub_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.154_sub_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2116160
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_730413_length_448_cov_1.983827"


✖ anvi-profile encountered an error after 0:00:07.722525


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_61786_length_1930_cov_4.763087'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.155_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.155.db
Contigs DB hash ...................................: hash12d75508
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.155.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.155_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.155_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118364
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_659841_length_483_cov_2.795567"


✖ anvi-profile encountered an error after 0:00:07.479384


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_1314_length_23565_cov_7.536231'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.28_sub_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.28_sub.db
Contigs DB hash ...................................: hash00629e06
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.28_sub.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.28_sub_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.28_sub_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2117583
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1863438_length_244_cov_2.215569"


✖ anvi-profile encountered an error after 0:00:07.622058


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_3542_length_11763_cov_6.414085'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.2_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.2.db
Contigs DB hash ...................................: hashd9fdedfa
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.2.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.2_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.2_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118427
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1623725_length_262_cov_2.000000"


✖ anvi-profile encountered an error after 0:00:07.584917


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_649_length_35924_cov_11.506402'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.68_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.68.db
Contigs DB hash ...................................: hash2a4cf7ea
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.68.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.68_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.68_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118578
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1280471_length_296_cov_2.018265"


✖ anvi-profile encountered an error after 0:00:07.436530


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_22020_length_3468_cov_5.763492'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.76_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.76.db
Contigs DB hash ...................................: hash5244ecd1
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.76.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.76_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.76_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2117201
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1357150_length_286_cov_3.153110"


✖ anvi-profile encountered an error after 0:00:07.609913


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_115004_length_1353_cov_5.039185'. You may be using
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.90_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.90.db
Contigs DB hash ...................................: hashecd7aaef
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.90.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.90_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.90_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118168
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_2066873_length_230_cov_6.248366"


✖ anvi-profile encountered an error after 0:00:07.630014


Config Error: At least one contig name in your BAM file does not match contig names stored in 
              the contigs database. For instance, this is one contig name found in your BAM   
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in    
              your contigs database: 'NODE_393_length_47673_cov_7.189785'. You may be using an
              contigs database for profiling that has nothing to do with the BAM file you are 
              trying to profile, or you may have failed to fix your contig names in your FASTA
              file prior to mapping, which is described here: http://goo.gl/Q9ChpS            


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.97_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.97.db
Contigs DB hash ...................................: hashecc30feb
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.concoct.97.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.97_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.concoct.97_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2117983
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1956334_length_238_cov_1.378882"


✖ anvi-profile encountered an error after 0:00:07.396119


Config Error: At least one contig name in your BAM file does not match contig names stored in 
              the contigs database. For instance, this is one contig name found in your BAM   
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in    
              your contigs database: 'NODE_8383_length_6303_cov_4.178124'. You may be using an
              contigs database for profiling that has nothing to do with the BAM file you are 
              trying to profile, or you may have failed to fix your contig names in your FASTA
              file prior to mapping, which is described here: http://goo.gl/Q9ChpS            


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.maxbin2.018_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.maxbin2.018.db
Contigs DB hash ...................................: hash079ed469
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.maxbin2.018.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.maxbin2.018_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.maxbin2.018_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118421
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1486719_length_273_cov_3.367347"


✖ anvi-profile encountered an error after 0:00:07.398030


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_252_length_59992_cov_10.920738'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.maxbin2.022_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.maxbin2.022.db
Contigs DB hash ...................................: hash4014fa35
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.maxbin2.022.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.maxbin2.022_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.maxbin2.022_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2117973
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1789411_length_249_cov_3.430233"


✖ anvi-profile encountered an error after 0:00:07.782506


Config Error: At least one contig name in your BAM file does not match contig names stored in 
              the contigs database. For instance, this is one contig name found in your BAM   
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in    
              your contigs database: 'NODE_5059_length_9000_cov_8.423848'. You may be using an
              contigs database for profiling that has nothing to do with the BAM file you are 
              trying to profile, or you may have failed to fix your contig names in your FASTA
              file prior to mapping, which is described here: http://goo.gl/Q9ChpS            


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.maxbin2.023_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.maxbin2.023.db
Contigs DB hash ...................................: hash200fd69a
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.maxbin2.023.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.maxbin2.023_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.maxbin2.023_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2117100
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1836902_length_246_cov_1.751479"


✖ anvi-profile encountered an error after 0:00:07.999201


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_13778_length_4596_cov_7.419562'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.10_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.10.db
Contigs DB hash ...................................: hashf6a0cb1a
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.10.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.10_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.10_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118675
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_214066_length_944_cov_1.592849"


✖ anvi-profile encountered an error after 0:00:07.399530


Config Error: At least one contig name in your BAM file does not match contig names stored in 
              the contigs database. For instance, this is one contig name found in your BAM   
              file: 'NODE_2_length_491939_cov_19.084225', and this is another one found in    
              your contigs database: 'NODE_5_length_331879_cov_19.303160'. You may be using an
              contigs database for profiling that has nothing to do with the BAM file you are 
              trying to profile, or you may have failed to fix your contig names in your FASTA
              file prior to mapping, which is described here: http://goo.gl/Q9ChpS            


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.25_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.25.db
Contigs DB hash ...................................: hash2fe274fe
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.25.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.25_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.25_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118575
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1250848_length_301_cov_1.553571"


✖ anvi-profile encountered an error after 0:00:07.421798


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_49893_length_2178_cov_8.041885'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.27_sub_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.27_sub.db
Contigs DB hash ...................................: hash9066ad0f
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.27_sub.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.27_sub_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.27_sub_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2117961
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_510166_length_570_cov_1.432049"


✖ anvi-profile encountered an error after 0:00:07.621136


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_18536_length_3841_cov_4.891605'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.31_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.31.db
Contigs DB hash ...................................: hash4756ec91
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.31.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.31_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.31_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118183
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_992086_length_355_cov_2.071942"


✖ anvi-profile encountered an error after 0:00:07.544744


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_68990_length_1811_cov_18.559400'. You may be using
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.3_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.3.db
Contigs DB hash ...................................: hasha28703a9
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.3.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.3_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.3_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118439
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1752380_length_252_cov_2.502857"


✖ anvi-profile encountered an error after 0:00:07.558282


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_4574_length_9757_cov_18.113120'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.43_sub_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.43_sub.db
Contigs DB hash ...................................: hashae0b15f1
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.43_sub.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.43_sub_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.43_sub_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2117978
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_60508_length_1954_cov_4.848162"


✖ anvi-profile encountered an error after 0:00:07.412404


Config Error: At least one contig name in your BAM file does not match contig names stored in 
              the contigs database. For instance, this is one contig name found in your BAM   
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in    
              your contigs database: 'NODE_9800_length_5684_cov_6.806314'. You may be using an
              contigs database for profiling that has nothing to do with the BAM file you are 
              trying to profile, or you may have failed to fix your contig names in your FASTA
              file prior to mapping, which is described here: http://goo.gl/Q9ChpS            


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.49_sub_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.49_sub.db
Contigs DB hash ...................................: hash950f2d11
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.49_sub.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.49_sub_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.49_sub_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118652
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_58397_length_1994_cov_2.948357"


✖ anvi-profile encountered an error after 0:00:07.699326


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_598_length_37912_cov_17.113440'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.53_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.53.db
Contigs DB hash ...................................: hasha1cf4d00
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.53.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.53_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.53_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118504
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1026737_length_346_cov_1.910781"


✖ anvi-profile encountered an error after 0:00:07.666008


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_1191_length_25167_cov_8.904026'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.55_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.55.db
Contigs DB hash ...................................: hashe8d767ad
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.55.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.55_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.55_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118591
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_2090866_length_229_cov_1.947368"


✖ anvi-profile encountered an error after 0:00:07.928789


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_41381_length_2423_cov_17.334186'. You may be using
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.56_sub_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.56_sub.db
Contigs DB hash ...................................: hash95227111
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.56_sub.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.56_sub_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.56_sub_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118275
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_2031689_length_233_cov_1.467949"


✖ anvi-profile encountered an error after 0:00:07.579535


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_43559_length_2355_cov_7.241001'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.58_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.58.db
Contigs DB hash ...................................: hash18433276
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.58.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.58_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.58_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118607
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_2018295_length_234_cov_1.235669"


✖ anvi-profile encountered an error after 0:00:07.369093


Config Error: At least one contig name in your BAM file does not match contig names stored in 
              the contigs database. For instance, this is one contig name found in your BAM   
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in    
              your contigs database: 'NODE_390_length_47896_cov_9.223949'. You may be using an
              contigs database for profiling that has nothing to do with the BAM file you are 
              trying to profile, or you may have failed to fix your contig names in your FASTA
              file prior to mapping, which is described here: http://goo.gl/Q9ChpS            


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.65_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.65.db
Contigs DB hash ...................................: hash2cae073c
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.65.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.65_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.65_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118515
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1354774_length_287_cov_1.057143"


✖ anvi-profile encountered an error after 0:00:07.451202


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_4808_length_9370_cov_12.452814'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS     


Sample name set ...................................: bb_2024_sorted
Description .......................................: None
Profile DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.75_sub_PROFILE/PROFILE.db
Contigs DB path ...................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.75_sub.db
Contigs DB hash ...................................: hash0210dbca
Command line ......................................: /usr/local/bioinfo/Anaconda3-23/envs/anvio-8/bin/anvi-profile -i /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam -c /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/01_db_create_0523/das_tool.metabat2.75_sub.db --output-dir /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.75_sub_PROFILE --num-threads 64

Minimum percent identity of reads to be profiled ..: None
Fetch filter engaged ..............................: None

Is merged profile? ................................: False
Is blank profile? .................................: False
Skip contigs shorter than .........................: 1,000
Skip contigs longer than ..........................: 9,223,372,036,854,775,807
Perform hierarchical clustering of contigs? .......: False

Profile single-nucleotide variants (SNVs)? ........: True
Profile single-codon variants (SCVs/+SAAVs)? ......: False
Profile insertion/deletions (INDELs)? .............: True
Minimum coverage to calculate SNVs ................: 10
Report FULL variability data? .....................: False

WARNING
====================================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

Input BAM .........................................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/05_mapping/02_bb_2024_k77_contigs/mappingoutput/bb_2024_sorted.bam
Output directory path .............................: /vol/micro-proj2/shiyi/metagenomics/w_wwtp/16_bin_refinement/01_bb_refinement_anvio/02_add_mapping_info5/das_tool.metabat2.75_sub_PROFILE

Number of reads in the BAM file ...................: 75,553,272
Number of sequences in the contigs DB .............: 2,118,707

WARNING
====================================================
According to the data generated in the contigs database, there are 2118247
contigs in your BAM file with 0 gene calls. Which may not be unusual if (a) some
of your contigs are very short, or (b) your the gene caller was not capable of
dealing with the type of data you had. If you would like to take a look
yourself, here is one contig that is missing any genes:
NODE_1510172_length_271_cov_2.546392"


✖ anvi-profile encountered an error after 0:00:07.928162


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_6274_length_7658_cov_22.811107'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS

from anvio.

meren commented on July 26, 2024

Hey @NebulaSL,

The key part of the error you're having is here:


Config Error: At least one contig name in your BAM file does not match contig names stored in
              the contigs database. For instance, this is one contig name found in your BAM  
              file: 'NODE_1_length_543061_cov_19.315573', and this is another one found in   
              your contigs database: 'NODE_21375_length_3530_cov_4.782508'. You may be using 
              an contigs database for profiling that has nothing to do with the BAM file you 
              are trying to profile, or you may have failed to fix your contig names in your 
              FASTA file prior to mapping, which is described here: http://goo.gl/Q9ChpS

You need to use the same FASTA file for read recruitment and the generation of contigs-db file. It seems the FASTA file you have used were not identical.

The best solution is to run the following on your input FASTA file first:

anvi-script-reformat-fasta contigs-input.fa -o contigs.fa -l 0 --simplify-names

And then use contigs.fa for read recruitment as well as with anvi-gen-contigs-database. It will fix this error.

Meren.

from anvio.

NebulaSL commented on July 26, 2024

it worked out in the end! thanks a lot @meren

from anvio.

meren commented on July 26, 2024

Great! 🙂

from anvio.

[BUG] created profile does not include a table named `mean_coverage_Q2Q3_splits` about anvio HOT 5 CLOSED

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