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Coprolite host Identification pipeline

Home Page: https://nf-co.re/coproid

License: MIT License

Python 20.65% Nextflow 67.87% Dockerfile 0.33% HTML 1.72% Jupyter Notebook 9.43%

adna ancient-dna coprolite microbiome nextflow nf-core pipeline workflow

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coproid's Issues

Channel error

Goodmorning,

After performing successfully the test, I am trying to run the pipeline using one sample but I get the following message

Channel bt1_chhas been used twice as an output by processBowtieIndexGenome1 and another operator

Not sure if it is a problem of nextflow or of coproid but I wonder if someone can help understanding what to do to resolve it.
Here is the command line I used
nextflow run maxibor/coproid --genome1 'GRCh37' --genome2 'CanFam3.1' --name1 'Homo_sapiens' --name2 'Canis_familiaris' --reads '/mnt/c/Users/Min/Desktop/CoproID/Copro-16_R{1,2}_001.fastq.gz' --krakendb '/mnt/d/IGenomes/minikraken2_v2_8GB.tgz' --igenomes_base '/mnt/d/IGenomes/' -profile docker

Thank you

Kraken2 segmentation fault with Conda install

See: kraken2/issues/222.
Installing Kraken2 via conda will lead to a Segfault when running it.
Waiting for a fix

$ conda list | grep kraken2
kraken2                   2.0.8_beta      pl526hc9558a2_1    bioconda
$ kraken2 --db kraken \
        --threads 2 \
        --output metagenome.kraken.out \
        --report metagenome.kreport metagenome_Bacillus_subtilis.unaligned.fastq
Loading database information... done.
Processed 72181 sequences (6588042 bp) ...Segmentation fault (core dumped)

Add Zenodo DOI for release to main README on master

Would be good to add the Zenodo DOI for the release to the main README of the pipeline in order to make it citable. You will have to do this via a branch pushed to the repo in order to directly update master. See PR below for example and file changes:
nf-core/atacseq#38

See https://zenodo.org/record/2653757#.XVZ0buhKhPY

Web-hooks are already set-up for this repo to have a unique Zenodo DOI generated everytime a new version of the pipeline is released. Would be good to add this in after every release 👍

Problem in the file download during Test run

Hi,

I am using nextflow version 20.10.0.5430 and I am trying to run the test run using command

nextflow run nf-core/coproid -profile test,docker

But I got the warnings reported below:

WARN: Unable to stage foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/coproid/kraken.tar.gz (try 1) -- Cause: No PSK available. Unable to resume. WARN: Unable to stage foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/coproid/genomes/bsubtilis/genome.fa (try 1) -- Cause: No PSK available. Unable to resume. WARN: Unable to stage foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/coproid/kraken.tar.gz (try 2) -- Cause: No PSK available. Unable to resume. WARN: Unable to stage foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/coproid/genomes/ecoli/genome.fa (try 1) -- Cause: No PSK available. Unable to resume. WARN: Unable to stage foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/coproid/kraken.tar.gz (try 3) -- Cause: No PSK available. Unable to resume. WARN: Unable to stage foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/coproid/genomes/bsubtilis/genome.fa (try 2) -- Cause: No PSK available. Unable to resume. WARN: Unable to stage foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/coproid/genomes/ecoli/genome.fa (try 2) -- Cause: No PSK available. Unable to resume. WARN: Unable to stage foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/coproid/genomes/bsubtilis/genome.fa (try 3) -- Cause: No PSK available. Unable to resume. WARN: Unable to stage foreign file: https://github.com/nf-core/test-datasets/raw/coproid/reads/metagenome.1.fastq.gz (try 1) -- Cause: No PSK available. Unable to resume.

This brings the program to abort due to the impossibility to download the files for the Test run.
I wanted to understand what went wrong. Is it just a problem of Nextflow version or something else is going on?

Thank you for your attention

an error on sourcepredict (test command)

Hi. Thank you for distributing the fantastic tool! I got the following error message about sourcepredict on the test command nextflow run nf-core/coproid -profile test,docker

executor >  local (34)
[24/bfa148] process > decomp_kraken                          [100%] 1 of 1 ✔
[58/8fb11a] process > fastqc (metagenomebis)                 [100%] 2 of 2 ✔
[4d/86e1a5] process > renameGenome1                          [100%] 1 of 1 ✔
[a2/c13f47] process > renameGenome2                          [100%] 1 of 1 ✔
[c6/f2701d] process > AdapterRemovalCollapse (metagenomebis) [100%] 2 of 2 ✔
[05/113fd2] process > BowtieIndexGenome1 (Bacillus_subtilis) [100%] 1 of 1 ✔
[27/80775b] process > AlignToGenome1 (metagenomebis)         [100%] 2 of 2 ✔
[42/d4ecff] process > bam2fq (metagenomebis)                 [100%] 2 of 2 ✔
[78/b187fb] process > BowtieIndexGenome2 (Escherichia_coli)  [100%] 1 of 1 ✔
[1c/f88ba9] process > AlignToGenome2 (metagenomebis)         [100%] 2 of 2 ✔
[c6/464bf6] process > pmdtoolsgenome1 (metagenomebis)        [100%] 2 of 2 ✔
[95/56f7a7] process > pmdtoolsgenome2 (metagenome)           [100%] 2 of 2 ✔
[f8/b912b0] process > kraken2 (metagenomebis)                [100%] 2 of 2 ✔
[e0/a30a0f] process > kraken_parse (metagenomebis)           [100%] 2 of 2 ✔
[c1/a5ef38] process > kraken_merge                           [100%] 1 of 1 ✔
[bb/135ba3] process > sourcepredict                          [100%] 1 of 1, failed: 1 ✘
[5b/0308e5] process > countBp2genomes (metagenomebis)        [100%] 2 of 2 ✔
[0a/b8525d] process > damageprofilerGenome1 (metagenomebis)  [100%] 2 of 2 ✔
[99/325890] process > damageprofilerGenome2 (metagenomebis)  [100%] 2 of 2 ✔
[-        ] process > concatenateRatios                      -
[-        ] process > generate_report_adna_2_genomes         -
[8a/d9c396] process > get_software_versions                  [100%] 1 of 1 ✔
[3d/f04710] process > multiqc                                [100%] 1 of 1 ✔
[45/bf327f] process > output_documentation                   [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/coproid] Pipeline completed with errors-
Error executing process > 'sourcepredict'

Caused by:
  Process `sourcepredict` terminated with an error exit status (1)

Command executed:

  sourcepredict -di 2 \
                -kne 0 \
                -me tsne \
                -n subsample \
                -l test_labels.csv \
                -s test_sources.csv \
                -t 2 \
                -o prediction.sourcepredict.csv \
                -e sourcepredict_embedding.csv kraken_merged.csv

Command exit status:
  1

Command output:
   2290000 generating entries... 
   2291000 generating entries... 
   2292000 generating entries... 
   2293000 generating entries... 
   2294000 generating entries... 
   2295000 generating entries... 
   2296000 generating entries... 
   2297000 generating entries... 
   2298000 generating entries... 
   2299000 generating entries... 
   2300000 generating entries... 
   2301000 generating entries... 
   2302000 generating entries... 
   2303000 generating entries... 
   2304000 generating entries... 
   2305000 generating entries... 
   2306000 generating entries... 
   2307000 generating entries... 
   2308000 generating entries... 
   2309000 generating entries... 
   2310000 generating entries... 
   2311000 generating entries... 
   2312000 generating entries... 
   2313000 generating entries... 
   2314000 generating entries... 
   2315000 generating entries... 
   2316000 generating entries... 
   2317000 generating entries... 
   2318000 generating entries... 
   2319000 generating entries... 
   2320000 generating entries... 
   2321000 generating entries... 
   2322000 generating entries... 
   2323000 generating entries... 
   2324000 generating entries... 
   2325000 generating entries... 
   2326000 generating entries... 
   2327000 generating entries... 
   2328000 generating entries... 
   2329000 generating entries... 
   2330000 generating entries... 
   2331000 generating entries... 
   2332000 generating entries... 
   2333000 generating entries... 
   2334000 generating entries... 
   2335000 generating entries... 
   2336000 generating entries... 
   2337000 generating entries... 
  Uploading to /tmp/.etetoolkit/taxa.sqlite

Command error:
  NCBI database not present yet (first time used?)
  Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
  Done. Parsing...
  
  Inserting synonyms:          0 
  Inserting synonyms:       5000 
  Inserting synonyms:      10000 
  Inserting synonyms:      15000 
  Inserting synonyms:      20000 
  Inserting synonyms:      25000 
  Inserting synonyms:      30000 
  Inserting synonyms:      35000 Traceback (most recent call last):
    File "/opt/conda/envs/nf-core-coproid-1.1/bin/sourcepredict", line 10, in <module>
      sys.exit(main())
    File "/opt/conda/envs/nf-core-coproid-1.1/lib/python3.7/site-packages/sourcepredict/__main__.py", line 172, in main
      sm.compute_distance(distance_method=distance_method, rank=RANK)
    File "/opt/conda/envs/nf-core-coproid-1.1/lib/python3.7/site-packages/sourcepredict/sourcepredictlib/ml.py", line 251, in compute_distance
      ncbi = NCBITaxa()
    File "/opt/conda/envs/nf-core-coproid-1.1/lib/python3.7/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 110, in __init__
      self.update_taxonomy_database(taxdump_file)
    File "/opt/conda/envs/nf-core-coproid-1.1/lib/python3.7/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 129, in update_taxonomy_database
      update_db(self.dbfile)
    File "/opt/conda/envs/nf-core-coproid-1.1/lib/python3.7/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 760, in update_db
      upload_data(dbfile)
    File "/opt/conda/envs/nf-core-coproid-1.1/lib/python3.7/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 802, in upload_data
      db.execute("INSERT INTO synonym (taxid, spname) VALUES (?, ?);", (taxid, spname))
  sqlite3.IntegrityError: UNIQUE constraint failed: synonym.spname, synonym.taxid

Work dir:
  /home/cae803/opt/coproid/work/bb/135ba36e56db6c94bd9694208e094d

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

How do I fix it? I don't have the directory /opt/conda/ in my workstation. I am looking forward to using coproid!

Logo uses the wrong font

New logo is great, but it's been created without the correct font. You need Maven Pro Bold installed before you generate it - see Logo Requirements

NB: Same as nf-core/hic#12 and lots of other places. We should really make a docker container or something that has all of the requirements so that people don't fall in to this trap. (@maxulysse has been talking about it for a while now 😆)

Update Pipeline to Nextflow DSL2

Hi @everyone,

I tried running the nf-core/coproid pipeline with this command:
nextflow run nf-core/coproid -r 1.1.1 -profile test,docker --outdir <output dir>

But I got this error:
Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier

It'd be great, if you would consider to update the pipeline to Nextflow DSL2 to avoid issues with newer Nextflow versions.

Thanks!

Cheers, Meret

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