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nf-core / mag

Assembly and binning of metagenomes
https://nf-co.re/mag
MIT License
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BUSCO error: `Either --summaries_domain, --summaries_specific or --failed_bins must be specified!` #468

Closed bioforkgithub closed 1 year ago

bioforkgithub commented 1 year ago

Description of the bug

I have downloaded the BUSCO datadase and whenever i give the local path to the folder this is the error i get

Command used and terminal output

[nf-core/mag] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_MAG:MAG:BUSCO_QC:BUSCO_SUMMARY'

Caused by:
  Process `NFCORE_MAG:MAG:BUSCO_QC:BUSCO_SUMMARY` terminated with an error exit status (1)

Command executed:

  summary_busco.py -a    -o busco_summary.tsv

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_MAG:MAG:BUSCO_QC:BUSCO_SUMMARY":
      python: $(python --version 2>&1 | sed 's/Python //g')
      pandas: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('pandas').version)")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  Either --summaries_domain, --summaries_specific or --failed_bins must be specified!
  INFO:    Cleaning up image...

Work dir:
  /gpfs/gpfs0/prosjekt/.prosjekt2/15719-Res-Marine/workingspace/sra_data/_13_svalbard/sample9/S9R2/Sample_18-WWR2/work/84/ae5bf0208b290098b73fe10dace310

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

 -- Check '.nextflow.log' file for details

Relevant files

Jul-04 13:18:56.561 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /localsoftware/nf-core-mag_2.3.2/2_3_2/ -profile singularity --input samples.csv --outdir nf-core_result --multiqc_title MULTIQC --centrifuge_db /gpfs/gpfs0/felles/fres/MY_CENTRIFUGE_DB/hpvc.tar.gz --skip_spades --skip_spadeshybrid --busco_clean --refine_bins_dastool --ancient_dna true Jul-04 13:18:56.633 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.1 Jul-04 13:18:56.650 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/a40540/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.2 Jul-04 13:18:56.659 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Jul-04 13:18:56.659 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Jul-04 13:18:56.663 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Jul-04 13:18:56.673 [main] INFO org.pf4j.AbstractPluginManager - No plugins Jul-04 13:18:57.541 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /localsoftware/nf-core-mag_2.3.2/2_3_2/nextflow.config Jul-04 13:18:57.542 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /localsoftware/nf-core-mag_2.3.2/2_3_2/nextflow.config Jul-04 13:18:57.549 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: singularity Jul-04 13:18:58.375 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, uge, rosalind_uge, lugh, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, tigem, tubingen_apg, google, ipop_up, googlels, eddie, medair, test_host_rm, bi, bigpurple, sbc_sharc, adcra, cedars, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, test_ancient_dna, ceres, munin, arm, rosalind, test_binrefinement, hasta, cfc, uzh, test_hybrid_host_rm, test_busco_auto, ebc, ku_sund_dangpu, ccga_dx, test_hybrid, crick, marvin, biohpc_gen, shifter, mana, mamba, wehi, awsbatch, imperial, maestro, genotoul, test_no_clipping, abims, janelia, nihbiowulf, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, sage, cambridge, podman, cheaha, xanadu, test, computerome, seg_globe, sanger, dkfz, pasteur, test_full, azurebatch, hki, test_adapterremoval, crukmi, docker, engaging, gis, hypatia, psmn, eva, fgcz, conda, crg, singularity, prince, utd_sysbio, debug, genouest, cbe, phoenix, gitpod, seawulf, uct_hpc, aws_tower, binac] Jul-04 13:18:58.412 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Jul-04 13:18:58.425 [main] INFO nextflow.cli.CmdRun - Launching /localsoftware/nf-core-mag_2.3.2/2_3_2/main.nf [big_saha] DSL2 - revision: 8f9adbafb4 Jul-04 13:18:58.426 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Jul-04 13:18:58.426 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Jul-04 13:18:58.432 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/a40540/.nextflow/secrets/store.json Jul-04 13:18:58.434 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@b01cb8d] - activable => nextflow.secret.LocalSecretsProvider@b01cb8d Jul-04 13:18:58.479 [main] DEBUG nextflow.Session - Session UUID: baa2de72-89e8-4e96-ae9d-ca332d62785f Jul-04 13:18:58.479 [main] DEBUG nextflow.Session - Run name: big_saha Jul-04 13:18:58.480 [main] DEBUG nextflow.Session - Executor pool size: 256 Jul-04 13:18:58.489 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=768; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jul-04 13:18:58.511 [main] DEBUG nextflow.cli.CmdRun - Version: 23.04.1 build 5866 Created: 15-04-2023 06:51 UTC (08:51 CEST) ".nextflow.log" 505L, 88501B

System information

Nextflow version ( 23.04.1) Hardware (local server) Executor (local) Container engine: (Singularity) OS (CentOS) Version of nf-core/mag (2.3.2)

jfy133 commented 1 year ago

@bioforkgithub could you please provide the actual .nextflow.log file?

I see you're running aDNA mode, from the limit logging information, my only thought is if none enough bins were generated for binning refinement (meaning the BUSCO filesweren't generated and couldn't reach the BUSCO summary)

I see you are running a local physical copy of the pipeline (/localsoftware/nf-core-mag_2.3.2/2_3_2/) rather than using the official nextflow pull nf-core/mag -r 2.3.2 can you confirm you've not modified this in any way?

bioforkgithub commented 1 year ago

/localsoftware/nf-core-mag_2.3.2/2_3_2/ . here the localsoftware is the name of my drive where I usually save all the git downloads. Ok I will check for busco because even though I am changing it to run checkm, busco is running is always showing up. No i havent changes any files after download. And ihave followed the instructions on the github about the installation.

And the 'Relevant file' section above is the ./nextflow.log file

jfy133 commented 1 year ago

@bioforkgithub Ok... not sure I follow as you're meant to get nextflow pipeliens with nextflow pull which then pulls to $NXF_HOME/assets/nf-core/<pipeline> - you shouldn't really git clone nextflow pipelines (even if you technically you can), but fair enough if you've not changed anything.

The relevant file section above isn't the actual file - you've just pasted the first X number of lines (from a terminal editor like vim by the looks of it?), so if you could upload the actual .nextflow.log file I should have all the info I need.

bioforkgithub commented 1 year ago

Maybe there was an issue with my system. It worked on my friends system. Thankyou.