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epi2me-labs / wf-metagenomics

Metagenomic classification of long-read sequencing data
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minimap error only when sample sheet is used #81

Closed irc47 closed 1 month ago

irc47 commented 4 months ago

Operating System

Windows 11

Other Linux

No response

Workflow Version

v2.6.1

Workflow Execution

EPI2ME Desktop application

EPI2ME Version

v5.1.9

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

I am running the workflow using minimap2 and attempting to add a sample sheet which I have done successfully in the past. The workflow will complete without the sample sheet. When I include the sheet, it passes sample sheet validation but encounters an error once it gets to the minimap steps:

ERROR ~ Error executing process > 'minimap_pipeline:minimap (21)' Caused by: Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

Perhaps there is just something wrong with the sample sheet? sample_alias_NP10.csv

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/mnt/c/Users/ilana/epi2melabs/workflows/epi2me-labs/wf-metagenomics/main.nf` [test_with_sample_id] DSL2 - revision: b3b2bd30a2
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-metagenomics v2.6.1
--------------------------------------------------------------------------------
Core Nextflow options
  runName        : test_with_sample_id
  containerEngine: docker
  launchDir      : /mnt/c/Users/ilana/epi2melabs/instances/wf-metagenomics_01HPF2K27WNVZ5GSHAWMX2BQDD
  workDir        : /mnt/c/Users/ilana/epi2melabs/instances/wf-metagenomics_01HPF2K27WNVZ5GSHAWMX2BQDD/work
  projectDir     : /mnt/c/Users/ilana/epi2melabs/workflows/epi2me-labs/wf-metagenomics
  userName       : epi2mewsl
  profile        : standard
  configFiles    : /mnt/c/Users/ilana/epi2melabs/workflows/epi2me-labs/wf-metagenomics/nextflow.config
Input Options
  fastq          : /mnt/c/Users/ilana/Documents/Science/Lab_Work/DNA_Sequencing/Nanopore/NP10_1117/basecalling/pass
  classifier     : minimap2
Sample Options
  sample_sheet   : /mnt/c/Users/ilana/Documents/Science/Lab_Work/Lab Projects/1117- syncom pilot 2023/sample_alias_NP10.csv
Reference Options
  store_dir      : /mnt/c/Users/ilana/epi2melabs/data
  database_sets  : [ncbi_16s_18s:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna, refindex:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna.fai, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_kraken2.tar.gz, kmer_dist:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/database1000mers.kmer_distrib, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ref2taxid.targloci.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], ncbi_16s_18s_28s_ITS:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna, refindex:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna.fai, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS_kraken2.tar.gz, kmer_dist:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/database1000mers.kmer_distrib, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ref2taxid.ncbi_16s_18s_28s_ITS.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], SILVA_138_1:[database:null], PlusPF-8:[database:https://genome-idx.s3.amazonaws.com/kraken/k2_pluspf_08gb_20230314.tar.gz, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip], PlusPFP-8:[database:https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_08gb_20230314.tar.gz, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip]]
Output Options
  out_dir        : /mnt/c/Users/ilana/epi2melabs/instances/wf-metagenomics_01HPF2K27WNVZ5GSHAWMX2BQDD/output
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-metagenomics for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-metagenomics v2.6.1.
--------------------------------------------------------------------------------
Checking inputs.
Checking fastq input.
[70/c10c40] Submitted process > minimap_pipeline:run_common:getParams
[c3/32eadc] Submitted process > minimap_pipeline:run_common:getVersions
[c7/7fb473] Submitted process > validate_sample_sheet
[4a/6c8892] Submitted process > minimap_pipeline:output (1)
Staging foreign file: https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip
Staging foreign file: https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna
[05/74f0d2] Submitted process > minimap_pipeline:output (2)
[2d/47cd08] Submitted process > minimap_pipeline:unpackTaxonomy
[a2/64a9fa] Submitted process > minimap_pipeline:check_reference_ref2taxid
WARN: Input directory 'barcode24' was found, but sample sheet '/mnt/c/Users/ilana/Documents/Science/Lab_Work/Lab Projects/1117- syncom pilot 2023/sample_alias_NP10.csv' has no such entry.
[90/877d01] Submitted process > fastcat (11)
[73/f350ea] Submitted process > fastcat (3)
[a2/fb7acb] Submitted process > fastcat (4)
[a9/edd293] Submitted process > fastcat (10)
[d6/e97eb8] Submitted process > minimap_pipeline:minimap (2)
[74/f6c040] Submitted process > fastcat (1)
[ad/309b35] Submitted process > fastcat (8)
[84/301afb] Submitted process > fastcat (2)
[17/b6adee] Submitted process > fastcat (12)
[f9/59bc4f] Submitted process > fastcat (9)
[67/8e3641] Submitted process > fastcat (6)
[7b/189f4c] Submitted process > fastcat (5)
[1a/36ebd8] Submitted process > fastcat (7)
[52/cae4ab] Submitted process > fastcat (13)
[f4/eeac8c] Submitted process > fastcat (15)
[39/77ba56] Submitted process > fastcat (14)
[d4/15599e] Submitted process > fastcat (16)
[8a/96252b] Submitted process > fastcat (17)
[93/21bfb4] Submitted process > fastcat (20)
[6e/97df50] Submitted process > fastcat (19)
[52/c910a1] Submitted process > fastcat (18)
[3a/aecd78] Submitted process > minimap_pipeline:minimap (1)
[a5/674bdd] Submitted process > minimap_pipeline:minimap (3)
ERROR ~ Error executing process > 'minimap_pipeline:minimap (21)'
Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
 -- Check '/mnt/c/Users/ilana/epi2melabs/instances/wf-metagenomics_01HPF2K27WNVZ5GSHAWMX2BQDD/nextflow.log' file for details
[79/e5d65d] Submitted process > minimap_pipeline:minimap (4)
WARN: Killing running tasks (4)

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

other (please describe below)

Other demo data information

Did not try but I did confirm that it works on my data without the sample sheet
nggvs commented 4 months ago

Hi @irc47 , First of all, thank you for using the workflow! I'll take a look in your issue, thank you for clarifying that it works without the sample_sheet. I've realised that you are using a previous version of the workflow, is there any reason for that?

Thank you very much in advance

irc47 commented 4 months ago

Hi Natalia, Thank you - I didn't realize that I was using a previous version but I now see that an update is available. I will update and retry. -Ilana

From: Natalia Garcia Garcia @.> Sent: Saturday, February 17, 2024 2:51 PM To: epi2me-labs/wf-metagenomics @.> Cc: Ilana Cohen @.>; Mention @.> Subject: [EXTERNAL]Re: [epi2me-labs/wf-metagenomics] minimap error only when sample sheet is used (Issue #81)

ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.

Hi @irc47https://github.com/irc47 , First of all, thank you for using the workflow! I'll take a look in your issue, thank you for clarifying that it works without the sample_sheet. I've realised that you are using a previous version of the workflow, is there any reason for that?

Thank you very much in advance

- Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-metagenomics/issues/81#issuecomment-1950293998, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BGDH5MLEKZINWMEHYDCVY5TYUECZBAVCNFSM6AAAAABDFDI7UCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJQGI4TGOJZHA. You are receiving this because you were mentioned.Message ID: @.***>

nggvs commented 4 months ago

Hi @irc47 , Thank you for retrying with the new version, please let me know if that fixes it or let me know if you are still experiencing the same issue.

irc47 commented 4 months ago

Hi Natalia, Thank you for checking in - I have updated both Epi2me Labs and the metagenomics workflow but I am still having the same issue (now with a different data set). The workflow completes with the files only but ends with an error when I add a sample sheet. I've attached my most recent log file, the report from that run and the sample sheet that I was using. Thank you for looking into this! -Ilana

From: Natalia Garcia Garcia @.> Sent: Saturday, February 24, 2024 5:39 AM To: epi2me-labs/wf-metagenomics @.> Cc: Ilana Cohen @.>; Mention @.> Subject: [EXTERNAL]Re: [epi2me-labs/wf-metagenomics] minimap error only when sample sheet is used (Issue #81)

ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.

Hi @irc47https://github.com/irc47 , Thank you for retrying with the new version, please let me know if that fixes it or let me know if you are still experiencing the same issue.

- Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-metagenomics/issues/81#issuecomment-1962324002, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BGDH5MIYUCEIVYD6WAUS2QDYVG7LBAVCNFSM6AAAAABDFDI7UCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRSGMZDIMBQGI. You are receiving this because you were mentioned.Message ID: @.***>

nggvs commented 1 month ago

Hi @irc47 , Apologies for the late answer, are you still having this issue?

irc47 commented 1 month ago

Thanks for checking in – no this issue seems to have gone away. I’m not sure what solved it. -Ilana

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From: Natalia Garcia Garcia @.> Sent: Thursday, June 6, 2024 8:20:55 AM To: epi2me-labs/wf-metagenomics @.> Cc: Ilana Cohen @.>; Mention @.> Subject: [EXTERNAL]Re: [epi2me-labs/wf-metagenomics] minimap error only when sample sheet is used (Issue #81)

ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.

Hi @irc47https://github.com/irc47 , Apologies for the late answer, are you still having this issue?

— Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-metagenomics/issues/81#issuecomment-2152464723, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BGDH5MOOASDHOZZNERZY5P3ZGBO3PAVCNFSM6AAAAABDFDI7UCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJSGQ3DINZSGM. You are receiving this because you were mentioned.Message ID: @.***>

nggvs commented 1 month ago

Glad to hear that! Thank you for using the workflow! I'll close the issue in that case