amarinderthind / decontaminer Goto Github PK

./collectInfo.sh -i /path/to/BACTERIA/COLLECTED_INFO/VALID

-- COLLECTING INFO --

INFO: organism type flag -V not specified. O(thers) assumed (default option).

• PROCESSING DETAILS
  INFO: processing NON virus data
  INFO: filtering with DEFAULT match count threshold 5.
  INFO: filtering terminated. Generating data Matrix

Processing sample IgG_S4, with total read counts: 571, valid reads: 571, others reads: 0
... finished.
Output files written in the directory:
/path/to/BACTERIA/COLLECTED_INFO/VALID

Processing sample IgG_S4, with total read counts: 571, valid reads: 571, others reads: 0
... finished.
Output files written in the directory:
/path/to/BACTERIA/COLLECTED_INFO/VALID

INFO: processing terminated. Generating HTML report

ERROR !! NO FILES IN THE DIRECTORY: /path/to/BACTERIA/COLLECTED_INFO/VALID/BACTERIA/COLLECTED_INFO
ERROR !! NO FILES IN THE DIRECTORY: /path/to/BACTERIA/COLLECTED_INFO/VALID/BACTERIA/COLLECTED_INFOINFO: processing terminated. Output files written in the dir /path/to/BACTERIA/COLLECTED_INFO/VALID/BACTERIA/HTML_REPORTS

Hi, I'm trying to run deconaMiner. The data I'm using is paired-end and in fastq format but as the manual says I merged the two fastqs. The problem is that when I try to run filterBlastInfo.sh I get this error

Format error on paired end names! Paired end should be numbered as xxx/1 and xxx/2 where xxx is the name of the query

I don't know if I'm merging the fastqs wrong or something, could you help me please?

Thanks!

Hi,

When I run filterBlastInfo.sh with paired end option, I found the following error.
Although the error said "Paired end should be numbered as xxx/1 and xxx/2", the name of blast table file was like "XXX1.table" or "XXXX1_vs_bacteria.table". What should I do to address this error?

filterBlastInfo.sh -i /media/.../decontaminer/RESULTS/BACTERIA

--------------output--------------
-- FILTERING BLAST RESULTS --

INFO: paired/single end flag -s not specified. PAIRED END assumed (default option).
INFO: organism type flag -V not specified. O(thers) assumed (default option).

• PROCESSING DETAILS
  INFO: processing PAIRED END data.
  INFO: processing NON virus alignments
  Processing file /media/.../decontaminer/RESULTS/BACTERIA/0_unmapped.1_vs_bacteria.table

Using L=read length G =0 M=0
Processing...

Format error on paired end names! Paired end should be numbered as xxx/1 and xxx/2 where xxx is the name of the query
--------------↑output--------------

Before filterBlastInfo.sh, I performed decontaMiner.sh using the paried end fastq files (0_unmapped.1.fastq, 0_unmapped.2.fastq). And in the directly RESULTS/BACTERIA, the files like 0_unmapped.1_vs_bacteria were generated.

Hi

I'm getting empty files after running collectInfo.sh. I think it is related to mineMicrobialData.pl.
Can you please advise on how to fix this error?

Thanks,

Lina

-- COLLECTING INFO --

INFO: organism type flag -V not specified. O(thers) assumed (default option).

• PROCESSING DETAILS
  INFO: processing NON virus data
  INFO: filtering with DEFAULT match count threshold 5.
  Can't open input file: No such file or directory at /decontaminer_out/decontaMiner_1.4/perl_scripts/mineMicrobialData.pl line 44.
  Can't open input file: No such file or directory at /decontaMiner_1.4/perl_scripts/mineMicrobialData.pl line 44.
  INFO: filtering terminated. Generating data Matrix

WARNING: No output was written Input files do not contain non-zero matches

WARNING: No output was written Input files do not contain non-zero matches
INFO: processing terminated. Generating HTML report

ERROR !! NO FILES IN THE DIRECTORY: /decontaminer_out/RESULTS/BACTERIA/COLLECTED_INFO
ERROR !! NO FILES IN THE DIRECTORY: /decontaminer_out/RESULTS/BACTERIA/COLLECTED_INFOINFO: processing terminated. Output files written in the dir decontaminer_out/RESULTS/BACTERIA/HTML_REPORTS

Dear authors,

Thank you for developing this nice tool. I would like to know how to interpret the output files of decontaminer and whether there is an option of your tool that visualizes the output of it.

Best regards,
Leonor

Hi,
I met a problem when I ran decontaMiner.sh. I just use your original databases and data(download from http://www-labgtp.na.icar.cnr.it/decontaminer/), but it said" ./Human_rna/rRNA.fasta, Human_rna/rRNA.idx is not an existing/valid absolute or relative path. I have checked the configure.txt, that's all right. Could you help me to solve the problem? Thank you so much!

Hey! I'm running decontaMiner with different parameters (filter_blastInfo) but it seems it's not letting me do it.
The parameters I'm setting are -g5 -m2 -l50 and the output says:

Using L=50G =2 M=2
Processing...
...done !

I can change -g to whatever and keeps telling me that, although if I change the length, it shows the correct set up.