Hello, First of all, congratulations on the development of Airrflow. I have used it successfully for several projects. However, I'm currently encountering an error that I can't resolve. I have consulted the Airrflow documentation as well as the GitHub repository, but I am unable to identify the cause of the problem. Specifically, I'm using Trust4 by Airrflow for a BCR analysis. This step has worked in the past, but in the context of this analysis, execution is automatically interrupted after 8 hours (Error :

Process exceeded running time limit (8h)

), even though I've set an upper limit in the

resource.config

file. Here's the error I'm encountering :

executor > local (2)
 [59/77eb5c] NFCORE_AIRRFLOW:AIRRFLOW:DATABASES:UNZIP_IGBLAST (unzip_db)                                     [100%] 1 of 1, cached: 1 ✔
 [6a/cc472a] NFCORE_AIRRFLOW:AIRRFLOW:DATABASES:UNZIP_REFERENCE_FASTA (unzip_db)                             [100%] 1 of 1, cached: 1 ✔
 [1a/d5604f] NFC…RRFLOW:AIRRFLOW:RNASEQ_INPUT:FASTQ_INPUT_CHECK:SAMPLESHEET_CHECK (assembled_samplesheet.tsv) [100%] 1 of 1, cached: 1 ✔
 [0e/e0172a] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:FASTP (BLOD_AM1_2_A1)                                     [100%] 2 of 2, cached: 2 ✔
 [75/d472ad] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:RENAME_FASTQ_TRUST4 (BLOD_AM1_2_A1)                       [100%] 2 of 2, cached: 2 ✔
 [c0/788e70] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:PREPARE_TRUST4_REFERENCE (BLOD_AM1_1_A1)                  [100%] 1 of 1, cached: 1 ✔
 [06/31e108] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:TRUST4 (BLOD_AM1_1_A1)                                    [100%] 2 of 2, failed: 2 ✘
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:CHANGEO_PARSEDB_SELECT_LOCUS                              -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:CHANGEO_CONVERTDB_FASTA_FROM_AIRR                         -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:CHANGEO_ASSIGNGENES                                     -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:CHANGEO_MAKEDB                                          -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:FILTER_QUALITY                                          -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:CHANGEO_PARSEDB_SPLIT                                   -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:FILTER_JUNCTION_MOD3                                    -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:ADD_META_TO_TAB                                         -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:BULK_QC_AND_FILTER:COLLAPSE_DUPLICATES                                 -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:SINGLE_CELL_QC_AND_FILTERING:SINGLE_CELL_QC                            -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:CLONAL_ANALYSIS:REPORT_THRESHOLD                                       -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:CLONAL_ANALYSIS:DEFINE_CLONES_COMPUTE                                  -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:CLONAL_ANALYSIS:DEFINE_CLONES_REPORT                                   -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:REPERTOIRE_ANALYSIS_REPORTING:REPORT_FILE_SIZE                         -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:REPERTOIRE_ANALYSIS_REPORTING:AIRRFLOW_REPORT                          -
 [-       ] NFCORE_AIRRFLOW:AIRRFLOW:MULTIQC                                                                -
 Execution cancelled -- Finishing pending tasks before exit
 -[nf-core/airrflow] Pipeline completed with errors-
 ERROR ~ Error executing process > 'NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:TRUST4 (BLOD_AM1_2_A1)'

 Caused by:
 Process exceeded running time limit (8h)


 Command executed:

 run-trust4 \
      \
      \
     -1 BLOD_AM1_2_A1_R1.fastq.gz -2 BLOD_AM1_2_A1_R2.fastq.gz \
      \
      \
      \
     -t 6 \
     -f trust4_reference.fa \
     -o BLOD_AM1_2_A1 \
      \

To make it easier for anyone to help, here is some additional information about this analysis : • Nextflow version :

version 24.10.3.5933

• File, resource.config :

process {
    resourceLimits = [cpus: 50, memory: 200.GB, time: 48.h]
    withName: 'NFCORE_AIRRFLOW:.*' { 
       time = '120.h'
    } 
}

(I also use only ressourceLimits, without "withName") • File, airrflow_sc_from_assembled.sh :

nextflow run nf-core/airrflow -r 4.3.0 \
-profile singularity \
--mode fastq \
--input assembled_samplesheet.tsv \
--library_generation_method trust4 \
--clonal_threshold 0.1 \
--outdir /mnt/DOSI/TDLAB/BIOINFO/Project/BLOD/BLOD_A1/05_Output/01_FlashPipe/02_Airrflow/ \
-resume

I also join the

assembled_samplesheet.tsv

file used for this analysis. Thank you in advance for your help, Kind regards

Hi Drystan, is it possible that you dont specify your config file? It's usually called using

-c resource.config

Indeed, this may be the reason. When copying my .sh I forgot to put it in. Thank you for your quick reply, I'll test this directly. I think I was too much in the project, or looking for the error...

Haha happy to help rubberducking rubber duck 😄 Maybe also try

withName: 'TRUST4'

or sth in this direction I never tried the

*

notation and dont know if this would work

Hello everyone, I'm back on this thread as the project remains the same, but I've encountered a new error when running the pipeline. All steps went correctly until ont of the final steps :

NFCORE_AIRRFLOW:AIRRFLOW:REPERTOIRE_ANALYSIS_REPORTING:REPORT_FILE_SIZE (file_size)

There seems to be a problem related to the size of the final output file, but I'm not sure. Please note : The error repeated several times, but did not immediately interrupt execution. So I'll provide, for help me to understand this error : An example of a repeated error that did not cause the pipeline to stop, and the final error that caused the shutdown. I'm continuing my research in parallel, but if anyone has any ideas or has already encountered this situation, I'd love to hear from you! Repeated error without code stoppage :

executor >  local (2)
[59/77eb5c] NFCORE_AIRRFLOW:AIRRFLOW:DATABASES:UNZIP_IGBLAST (unzip_db)                                      [100%] 1 of 1, cached: 1 ✔
[6a/cc472a] NFCORE_AIRRFLOW:AIRRFLOW:DATABASES:UNZIP_REFERENCE_FASTA (unzip_db)                              [100%] 1 of 1, cached: 1 ✔
executor >  local (6)
[59/77eb5c] NFCORE_AIRRFLOW:AIRRFLOW:DATABASES:UNZIP_IGBLAST (unzip_db)                                      [100%] 1 of 1, cached: 1 ✔
executor >  local (24)
[59/77eb5c] NFCORE_AIRRFLOW:AIRRFLOW:DATABASES:UNZIP_IGBLAST (unzip_db)                                      [100%] 1 of 1, cached: 1 ✔
[6a/cc472a] NFCORE_AIRRFLOW:AIRRFLOW:DATABASES:UNZIP_REFERENCE_FASTA (unzip_db)                              [100%] 1 of 1, cached: 1 ✔
[1a/d5604f] NFC…RRFLOW:AIRRFLOW:RNASEQ_INPUT:FASTQ_INPUT_CHECK:SAMPLESHEET_CHECK (assembled_samplesheet.tsv) [100%] 1 of 1, cached: 1 ✔
[0e/e0172a] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:FASTP (BLOD_AM1_2_A1)                                      [100%] 2 of 2, cached: 2 ✔
[8d/9b4a0b] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:RENAME_FASTQ_TRUST4 (BLOD_AM1_1_A1)                        [100%] 2 of 2, cached: 2 ✔
[43/de180c] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:PREPARE_TRUST4_REFERENCE (BLOD_AM1_2_A1)                   [100%] 1 of 1, cached: 1 ✔
[46/70d4d5] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:TRUST4 (BLOD_AM1_1_A1)                                     [100%] 2 of 2 ✔
[c0/918f42] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:CHANGEO_PARSEDB_SELECT_LOCUS (BLOD_AM1_1_A1)               [100%] 2 of 2 ✔
[1e/c63c82] NFCORE_AIRRFLOW:AIRRFLOW:RNASEQ_INPUT:CHANGEO_CONVERTDB_FASTA_FROM_AIRR (BLOD_AM1_1_A1)          [100%] 2 of 2 ✔
[7a/0f5f51] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:CHANGEO_ASSIGNGENES (BLOD_AM1_1_A1)                      [100%] 2 of 2 ✔
[0d/fce6fe] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:CHANGEO_MAKEDB (BLOD_AM1_1_A1)                           [100%] 2 of 2 ✔
[a3/8932d8] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:FILTER_QUALITY (BLOD_AM1_1_A1)                           [100%] 2 of 2 ✔
[24/d08b1d] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:CHANGEO_PARSEDB_SPLIT (BLOD_AM1_1_A1)                    [100%] 2 of 2 ✔
[0f/9cf394] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:FILTER_JUNCTION_MOD3 (BLOD_AM1_1_A1)                     [100%] 2 of 2 ✔
[60/d82c51] NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:ADD_META_TO_TAB (BLOD_AM1_1_A1)                          [100%] 2 of 2 ✔
[66/68c186] NFCORE_AIRRFLOW:AIRRFLOW:BULK_QC_AND_FILTER:COLLAPSE_DUPLICATES (BLOD_AM1_1_A1)                  [100%] 2 of 2 ✔
[-        ] NFCORE_AIRRFLOW:AIRRFLOW:SINGLE_CELL_QC_AND_FILTERING:SINGLE_CELL_QC                             -
[cf/275be0] NFCORE_AIRRFLOW:AIRRFLOW:CLONAL_ANALYSIS:REPORT_THRESHOLD (all_reps)                             [  0%] 0 of 1
[ca/098822] NFCORE_AIRRFLOW:AIRRFLOW:CLONAL_ANALYSIS:DEFINE_CLONES_COMPUTE (AM1_1_A1)                        [  0%] 0 of 2
[-        ] NFCORE_AIRRFLOW:AIRRFLOW:CLONAL_ANALYSIS:DEFINE_CLONES_REPORT                                    -
[d2/cbb5b8] NFCORE_AIRRFLOW:AIRRFLOW:REPERTOIRE_ANALYSIS_REPORTING:REPORT_FILE_SIZE (file_size)              [  0%] 0 of 1
[-        ] NFCORE_AIRRFLOW:AIRRFLOW:REPERTOIRE_ANALYSIS_REPORTING:AIRRFLOW_REPORT                           -
[-        ] NFCORE_AIRRFLOW:AIRRFLOW:MULTIQC                                                                 -
ERROR ~ Error executing process > 'NFCORE_AIRRFLOW:AIRRFLOW:REPERTOIRE_ANALYSIS_REPORTING:REPORT_FILE_SIZE (file_size)'

Caused by:
  Process `NFCORE_AIRRFLOW:AIRRFLOW:REPERTOIRE_ANALYSIS_REPORTING:REPORT_FILE_SIZE (file_size)` terminated with an error exit status (1)


Command executed:

  Rscript -e "enchantr::enchantr_report('file_size', \
          report_params=list('input'='all_logs_tabs.txt', 'metadata'='samplesheet.valid.tsv',\
          'outdir'=getwd()))"
 
      cp -r enchantr file_size_report && rm -rf enchantr
 
      echo ""NFCORE_AIRRFLOW:AIRRFLOW:REPERTOIRE_ANALYSIS_REPORTING:REPORT_FILE_SIZE":" > versions.yml
      Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'
  '))" >> versions.yml

Command exit status:
  1

Command output:
  1/26                   
  2/26 [global-options]  
  3/26                   
  4/26 [input-parameters]
  5/26 [unnamed-chunk-1]
  6/26                   
  7/26 [unnamed-chunk-2]
  8/26 [unnamed-chunk-3]
  9/26                   
  10/26 [unnamed-chunk-4]
  11/26                   
  12/26 [unnamed-chunk-5]

Command error:
  1/26                   
  2/26 [global-options]  
  3/26                   
  4/26 [input-parameters]
  5/26 [unnamed-chunk-1]
  6/26                   
  7/26 [unnamed-chunk-2]
  8/26 [unnamed-chunk-3]
  9/26                   
  10/26 [unnamed-chunk-4]
  11/26                   
  12/26 [unnamed-chunk-5]
  Error in `select()`:
  ! Can't select columns that don't exist.
  x Column `output` doesn't exist.
  Backtrace:
       x
    1. +-enchantr::getConsoleLogs(log_files)
    2. | +-dplyr::bind_rows(lapply(log_files, enchantr:::formatConsoleLog))
    3. | | \-rlang::list2(...)
    4. | \-base::lapply(log_files, enchantr:::formatConsoleLog)
    5. |   \-enchantr (local) FUN(X[[i]], ...)
    6. |     \-... %>% as.data.frame(stringsAsFactors = F)
    7. +-base::as.data.frame(., stringsAsFactors = F)