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EpiDiverse / wgbs

The EpiDiverse Whole Genome Bisulfite Sequencing Pipeline, implemented with Nextflow
MIT License
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WGBS:erne_bs5 (SRR5526206) unable to load (exit status: 127) #14

Open konetom opened 7 months ago

konetom commented 7 months ago

Hi, please I need help with this issue:

[7e/d74203] NOTE: Process `WGBS:erne_bs5 (SRR5526174)` terminated with an error exit status (127) -- Execution is retried (1)
[47/8108ab] NOTE: Process `WGBS:erne_bs5 (SRR5526206)` terminated with an error exit status (127) -- Execution is retried (1)
[bf/47a72f] NOTE: Process `WGBS:erne_bs5 (SRR5526209)` terminated with an error exit status (127) -- Execution is retried (1)
[61/698ace] NOTE: Process `WGBS:erne_bs5 (SRR5526172)` terminated with an error exit status (127) -- Execution is retried (1)
ERROR ~ Error executing process > 'WGBS:erne_bs5 (SRR5526174)'

Caused by:
  Process `WGBS:erne_bs5 (SRR5526174)` terminated with an error exit status (127)

Command executed:

executor >  local (6)
[-        ] process > WGBS:read_trimming              -
[-        ] process > WGBS:fastqc                     -
[d8/5d76f5] process > WGBS:erne_bs5 (SRR5526206)      [ 75%] 6 of 8, failed: 6, retries: 4
[-        ] process > WGBS:segemehl                   -
[-        ] process > WGBS:erne_bs5_processing        -
[-        ] process > WGBS:segemehl_processing        -
[-        ] process > WGBS:bam_merging                -
[-        ] process > WGBS:bam_subsetting             -
[-        ] process > WGBS:bam_filtering              -
[-        ] process > WGBS:bam_statistics             -
[-        ] process > CALL:bam_processing             -
[-        ] process > CALL:Picard_MarkDuplicates      -
[-        ] process > CALL:MethylDackel               -
[-        ] process > CALL:conversion_rate_estimation -
Execution cancelled -- Finishing pending tasks before exit
Oops... Pipeline execution stopped with the following message: null

         Pipeline execution summary
         ---------------------------
         Name         : maniac_tesla
         Profile      : conda
         Launch dir   : <path>
         Work dir     : <path> 
         Status       : failed
         Error report : Error executing process > 'WGBS:erne_bs5 (SRR5526174)'

Caused by:
  Process `WGBS:erne_bs5 (SRR5526174)` terminated with an error exit status (127)

Traced info:

task_id hash    native_id       name    status  exit    submit  duration        realtime        %cpu    peak_rss        peak_vmem       rchar   wchar
6       7e/d74203       11646   WGBS:erne_bs5 (SRR5526174)      FAILED  127     2024-01-25 13:23:19.202 138ms   129ms   -       -       -       -       -
10      47/8108ab       11649   WGBS:erne_bs5 (SRR5526206)      FAILED  127     2024-01-25 13:23:19.219 2.2s    2.1s    -       -       -       -       -
14      bf/47a72f       11779   WGBS:erne_bs5 (SRR5526209)      FAILED  127     2024-01-25 13:23:19.358 4s      4ms     -       -       -       -       -
3       61/698ace       11846   WGBS:erne_bs5 (SRR5526172)      FAILED  127     2024-01-25 13:23:21.396 4s      5ms     -       -       -       -       -
17      ea/be06b6       11924   WGBS:erne_bs5 (SRR5526174)      FAILED  127     2024-01-25 13:23:25.436 2s      3ms     -       -       -       -       -
18      d8/5d76f5       11994   WGBS:erne_bs5 (SRR5526206)      FAILED  127     2024-01-25 13:23:27.455 145ms   64ms    -       -       -       -       -
bio15anu commented 7 months ago

Hi Tomas, sorry you're having problems. Unfortunately there's not enough information here yet for me to be able to help you. First, did you try running the "Test data" example from the README? If this works correctly, then we know there is not a problem with the pipeline setup and configuration on your system. Then, please let me know how you are running the command on your own data and what files are present in the input directory. After that we can take a look at some further logging from the .nextflow.log file to see what's going on.