Error on Real Dataset - Githubissues

Hi, I'm running YAMP on a cluster, and here is my situation: I'm running YAMP on multiple samples, but each sample one by one. I ran the first few samples successfully. Now for some reason I get an error when I'm running even the previous samples that I ran successfully a while ago. I think this happened after a server maintenance. Now, I receive the following:

WARN: Killing pending tasks (1)

executor >  local (2)
[80/bf3d20] process > get_software_versions          [100%] 1 of 1, cached: 1 ✔
[-        ] process > dedup                          -
[9e/efe9da] process > remove_synthetic_contaminan... [100%] 1 of 1, cached: 1 ✔
[32/dda88f] process > trim (RCE_plus_DSS_301)        [  0%] 0 of 1
[93/6ee087] process > index_foreign_genome (1)       [100%] 1 of 1, cached: 1 ✔
[-        ] process > decontaminate                  -
[80/938ee3] process > quality_assessment (RCE_plu... [100%] 1 of 1, failed: 1 ✘
[-        ] process > merge_paired_end_cleaned       -
[-        ] process > profile_taxa                   -
[-        ] process > profile_function               -
[-        ] process > alpha_diversity                -
[-        ] process > log                            -
Error executing process > 'quality_assessment (RCE_plus_DSS_301)'

Caused by:
  Process `quality_assessment (RCE_plus_DSS_301)` terminated with an error exit status (1)

Command executed:

  fastqc -q input.1 input.2

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Skipping mount /curc/sw/singularity/3.6.4/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  Failed to process input.1
  uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@'
        at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158)
        at uk.ac.babraham.FastQC.Sequence.FastQFile.<init>(FastQFile.java:89)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:106)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:159)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:121)
        at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
  Failed to process input.2
  uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@'
        at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158)
        at uk.ac.babraham.FastQC.Sequence.FastQFile.<init>(FastQFile.java:89)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:106)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:159)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:121)
        at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)

Work dir:
  /gpfs/summit/scratch/parsa96@colostate.edu/YAMP/YAMP_Standard/YAMP/work/80/938ee3a35a22541b1baab053741e98

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`

I checked the input files to FastQC and they are empty for some reason! Has this happened before? Is there an easy solution for this problem?

Thanks

alesssia / YAMP

Error on Real Dataset #22