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epi2me-labs / wf-metagenomics

Metagenomic classification of long-read sequencing data
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Process `fastcat ` terminated with an error exit status (125) #102

Open aggath opened 1 month ago

aggath commented 1 month ago

Operating System

Windows 11

Other Linux

No response

Workflow Version

v2.10.0

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

v5.1.14

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

Something wrong with docker

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/mnt/c/Users/dnasec/epi2melabs/workflows/epi2me-labs/wf-metagenomics-2.10.0/main.nf` [modest_ritchie] DSL2 - revision: 6247543ce2
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-metagenomics v2.10.0
--------------------------------------------------------------------------------
Core Nextflow options
  runName              : modest_ritchie
  containerEngine      : docker
  launchDir            : /mnt/c/Users/dnasec/epi2melabs/instances/wf-metagenomics-2.10.0_01J012DTS9PE8EQXZSJE3WBGPC
  workDir              : /mnt/c/Users/dnasec/epi2melabs/instances/wf-metagenomics-2.10.0_01J012DTS9PE8EQXZSJE3WBGPC/work
  projectDir           : /mnt/c/Users/dnasec/epi2melabs/workflows/epi2me-labs/wf-metagenomics-2.10.0
  userName             : epi2mewsl
  profile              : standard
  configFiles          : /mnt/c/Users/dnasec/epi2melabs/workflows/epi2me-labs/wf-metagenomics-2.10.0/nextflow.config
Input Options
  fastq                : /mnt/c/data/WIMP_SEQ/240605_MEVGAL_DODONI_IOLI/20240605_1025_MN42159_FAZ27341_80640b9c/fastq_pass
  classifier           : minimap2
Reference Options
  database_set         : ncbi_16s_18s_28s_ITS
  store_dir            : /mnt/c/Users/dnasec/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, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_kraken2.tar.gz, 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, 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, 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], Standard-8:[database:https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20231009.tar.gz, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip], 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]]
Minimap2 Options
  minimap2_by_reference: true
Output Options
  out_dir              : /mnt/c/Users/dnasec/epi2melabs/instances/wf-metagenomics-2.10.0_01J012DTS9PE8EQXZSJE3WBGPC/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 v2.10.0.
--------------------------------------------------------------------------------
Checking inputs.
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Note: Empty files or those files whose reads have been discarded after filtering based on read length and/or read quality will not appear in the report and will be excluded from subsequent analysis.
Minimap2 pipeline.
Preparing databases.
Using default taxonomy database.
Using a default database.
[7b/351d5c] Submitted process > fastcat (3)
[e3/355375] Submitted process > fastcat (4)
[11/91fc19] Submitted process > minimap_pipeline:run_common:getVersions
[7b/481edb] Submitted process > fastcat (1)
[07/51b227] Submitted process > prepare_databases:download_reference_ref2taxid
[4e/299ca0] Submitted process > minimap_pipeline:run_common:getParams
[8e/94cbdb] Submitted process > fastcat (5)
[d2/982d26] Submitted process > prepare_databases:download_unpack_taxonomy
[d5/31eee1] Submitted process > fastcat (2)
ERROR ~ Error executing process > 'fastcat (3)'
Caused by:
  Process `fastcat (3)` terminated with an error exit status (125)
Command executed:
  mkdir fastcat_stats
  mkdir fastq_chunks

  # Save file as compressed fastq
  fastcat         -s barcode03         -f fastcat_stats/per-file-stats.tsv         -i fastcat_stats/per-file-runids.txt         --histograms histograms                           input_src     | if [ "0" = "0" ]; then
      bgzip -@ 4 > fastq_chunks/seqs.fastq.gz
    else
      split -l null -d --additional-suffix=.fastq.gz --filter='bgzip -@ 4 > $FILE' - fastq_chunks/seqs_;
    fi

  mv histograms/* fastcat_stats

  # get n_seqs from per-file stats - need to sum them up
  awk 'NR==1{for (i=1; i<=NF; i++) {ix[$i] = i}} NR>1 {c+=$ix["n_seqs"]} END{print c}'         fastcat_stats/per-file-stats.tsv > fastcat_stats/n_seqs
  # get unique run IDs
  awk 'NR==1{for (i=1; i<=NF; i++) {ix[$i] = i}} NR>1 {print $ix["run_id"]}'         fastcat_stats/per-file-runids.txt | sort | uniq > fastcat_stats/run_ids
Command exit status:
  125
Command output:
  (empty)
Command error:
  Unable to find image 'ontresearch/wf-common:sha338caea0a2532dc0ea8f46638ccc322bb8f9af48' locally
  docker: Error response from daemon: Head "https://registry-1.docker.io/v2/ontresearch/wf-common/manifests/sha338caea0a2532dc0ea8f46638ccc322bb8f9af48": Get "https://auth.docker.io/token?scope=repository%3Aontresearch%2Fwf-common%3Apull&service=registry.docker.io": net/http: TLS handshake timeout.
  See 'docker run --help'.
Work dir:
  /mnt/c/Users/dnasec/epi2melabs/instances/wf-metagenomics-2.10.0_01J012DTS9PE8EQXZSJE3WBGPC/work/7b/351d5cb8fd1b5c10e413dfb403c9d7
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/dnasec/epi2melabs/instances/wf-metagenomics-2.10.0_01J012DTS9PE8EQXZSJE3WBGPC/nextflow.log' file for details
WARN: Killing running tasks (1)

Application activity log entry

No response

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

no

Other demo data information

{
  "name": "Launch demo",
  "description": "Create a new workflow instance using demo data \n    that is downloaded from the internet",
  "updates": [
    {
      "message": "Checking workflow"
    },
    {
      "message": "Checking Windows version"
    },
    {
      "message": "WSL command exists, checking status"
    },
    {
      "message": "WSL is installed, checking version"
    },
    {
      "message": "Checking for updates to the EPI2ME distribution"
    },
    {
      "message": "WSL is ready to use."
    },
    {
      "message": "Checking Nextflow initialises"
    },
    {
      "message": "Nextflow is ready to use."
    },
    {
      "message": "All Setup tests are passing"
    },
    {
      "message": "Running demo for: epi2me-labs/wf-metagenomics-2.10.0"
    },
    {
      "message": "Error running cURL"
    }
  ],
  "id": "01J01430TFT1MKB799FHMMMHJQ",
  "percentage": 61,
  "status": "STOPPED_WITH_ERROR",
  "createdAt": "2024-06-10T13:06:06.287Z",
  "updatedAt": "2024-06-10T13:06:54.730Z",
  "metadata": {
    "trace": {
      "nxfCmd": "wsl",
      "nxfArgs": [
        "-d",
        "epi2me",
        "/mnt/c/Users/dnasec/AppData/Local/EPI2ME/app-5.1.14/resources/nextflow-all",
        "-h"
      ],
      "nxfExitCode": "0",
      "curlExitCode": 35,
      "curlStdout": "",
      "curlStderr": "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n                                 Dload  Upload   Total   Spent    Left  Speed\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:04 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:05 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:06 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:07 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:08 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:09 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:10 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:11 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:12 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:13 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:14 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:15 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:16 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:17 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:18 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:19 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:20 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:21 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:22 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:23 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:24 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:25 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:26 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:27 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:28 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:29 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:30 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:31 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:32 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:33 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:34 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:35 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:36 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:37 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:38 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:39 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:40 --:--:--     0\ncurl: (35) error:0A000126:SSL routines::unexpected eof while reading",
      "trace": "Non-zero exit status"
    },
    "track": {
      "windowsVersion": [
        "10",
        "0",
        "22631"
      ],
      "windowsRelease": 2009,
      "wslVersion": "2.1.5",
      "workflowName": "epi2me-labs/wf-metagenomics-2.10.0"
    }
  }
}
nggvs commented 1 month ago

Hi @aggath , It seems that the problem is downloading the docker images: Unable to find image 'ontresearch/wf-common:sha338caea0a2532dc0ea8f46638ccc322bb8f9af48' locally, you have internet when running the workflow? I have noticed that your version of EPI2ME is not updated, you may want to update to get the latest updates: https://labs.epi2me.io/downloads/

aggath commented 1 month ago

Hi @nggvs,

both the workflow and Epi2Me are fully updated to their latest versions. I do have internet connection. I understand that this has something to do with docker but since I have 0 knowledge of bioinformatics, I don't know how to solve this. Any suggestions?

nggvs commented 1 month ago

Hi, Sorry about the confusion, I thought it was version 5.1.4. I'll take a look on it. Thank you for using the workflow!

nggvs commented 1 month ago

Hi @aggath , Could you tried to download another workflow (for example wf-alignment?) and tell me if you also get the same error? Or retry demo on wf-metagenomics? Thank you in advance

aggath commented 1 month ago

Dear @nggvs,

I tried with wf-16S. The same error occurred.

Command error: Unable to find image 'ontresearch/wf-common:sha645176f98b8780851f9c476a064d44c2ae76ddf6' locally docker: Error response from daemon: Head "https://registry-1.docker.io/v2/ontresearch/wf-common/manifests/sha645176f98b8780851f9c476a064d44c2ae76ddf6": Get "https://auth.docker.io/token?scope=repository%3Aontresearch%2Fwf-common%3Apull&service=registry.docker.io": net/http: TLS handshake timeout. See 'docker run --help'. Work dir: /mnt/c/Users/dnasec/epi2melabs/instances/wf-16s_01J014K0G379W3W1P266908V25/work/82/23987cf4a74bb27810f9f5b359f640 Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run -- Check '/mnt/c/Users/dnasec/epi2melabs/instances/wf-16s_01J014K0G379W3W1P266908V25/nextflow.log' file for details [47/f0d489] Submitted process > prepare_databases:download_reference_ref2taxid [e9/7560ea] Submitted process > prepare_databases:download_unpack_taxonomy WARN: Killing running tasks (9)

nggvs commented 2 weeks ago

Hi @aggath, Apologies for the late answer, are you using a proxy or on a network with self signed certificate? Could you check if news articles are loading in the app?

Thank you very much in advance!