Test run fails during ProteomicsLFQ - file not found ("dev" version)

[hendrikweisser]

The current "dev" version of the workflow fails for me on the self-test data. The log output is included below (as part of "pipeline_report.txt") , but the cause of the problem isn't apparent from it. Digging through files in the work dir, the "proteomicslfq.log" seems to contain the relevant error message. This indicates that the first file given by a URL in the "experimental_design.tsv" could not be found (although the mzML file itself has been staged correctly). The problem looks related to #166.

proteomicslfq.log:

Removed 0 files from design to match given subset.
Performing feature intensity-based quantification.
Error: File not found (the file 'https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/BSA1_F1.mzML' could not be found)

pipeline_report.txt:

----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~\
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/proteomicslfq v1.1.0dev
----------------------------------------------------

Run Name: tender_shirley

####################################################
## nf-core/proteomicslfq execution completed unsuccessfully! ##
####################################################
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:

Error executing process > 'proteomicslfq (1)'

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

Command executed:

  ProteomicsLFQ -in BSA3_F1.mzML BSA2_F1.mzML BSA1_F2.mzML BSA1_F1.mzML BSA3_F2.mzML BSA2_F2.mzML \
                -ids BSA3_F1_msgf_idx_fdr_idpep_switched_filter.idXML BSA2_F1_msgf_idx_fdr_idpep_switched_filter.idXML BSA1_F2_msgf_idx_fdr_idpep_switched_filter.idXML BSA1_F1_msgf_idx_fdr_idpep_switched_filter.idXML BSA3_F2_msgf_idx_fdr_idpep_switched_filter.idXML BSA2_F2_msgf_idx_fdr_idpep_switched_filter.idXML \
                -design experimental_design.tsv \
                -fasta 18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta \
                -protein_inference aggregation \
                -quantification_method feature_intensity \
                -targeted_only true \
                -mass_recalibration false \
                -transfer_ids false \
                -protein_quantification unique_peptides \
                -alignment_order star \
                -out out.mzTab \
                -threads 2 \
                -out_msstats out_msstats.csv \
                -out_triqler out_triqler.tsv \
                -PeptideQuantification:quantify_decoys \
                -out_cxml out.consensusXML \
                -proteinFDR 1.0 \
                -debug 0 \
                > proteomicslfq.log

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.

Work dir:
  /home/hendrik.weisser/Data/Proteomics/SST/ProteomicsLFQ/work/50/84de930fa027607b25dad07ad3259c

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`

The workflow was completed at 2022-03-23T19:15:29.127Z (duration: 1m 7s)

The command used to launch the workflow was as follows:

  nextflow run nf-core/proteomicslfq -r dev -profile test,docker

Pipeline Configuration:
-----------------------
 - Pipeline Release: dev
 - Run Name: tender_shirley
 - Input: https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/BSA_design_urls.tsv
 - Max Resources: 6 GB memory, 2 cpus, 2d time per job
 - Container: docker - nfcore/proteomicslfq:dev
 - Output dir: ./results
 - Launch dir: /home/hendrik.weisser/Data/Proteomics/SST/ProteomicsLFQ
 - Working dir: /home/hendrik.weisser/Data/Proteomics/SST/ProteomicsLFQ/work
 - Script dir: /home/hendrik.weisser/.nextflow/assets/nf-core/proteomicslfq
 - User: hendrik.weisser
 - Config Profile: test,docker
 - Config Profile Description: Minimal test dataset to check pipeline function
 - Config Files: /home/hendrik.weisser/.nextflow/assets/nf-core/proteomicslfq/nextflow.config
 - Date Started: 2022-03-23T19:14:21.722Z
 - Date Completed: 2022-03-23T19:15:29.127Z
 - Pipeline script file path: /home/hendrik.weisser/.nextflow/assets/nf-core/proteomicslfq/main.nf
 - Pipeline script hash ID: 9390e9ba1e5b304e0f03f60f2642952a
 - Pipeline repository Git URL: https://github.com/nf-core/proteomicslfq
 - Pipeline repository Git Commit: b7c5ff0e6b7cf77cba870023b1ad3c8ab70134cd
 - Pipeline Git branch/tag: dev
 - Nextflow Version: 21.04.3
 - Nextflow Build: 5560
 - Nextflow Compile Timestamp: 21-07-2021 15:09 UTC

--
nf-core/proteomicslfq
https://github.com/nf-core/proteomicslfq

[jpfeuffer]

I think the nfcore/proteomicdslfq container was not uptodate. Can you do docker pull nfcore/proteomicslfq:dev and try again?

[hendrikweisser]

Thanks, Julianus. That indeed made it work. So when is it necessary to update the container using docker pull (on top of updating the pipeline using nextflow pull)?