``` Missing output file(s) `*.html` expected by pr...
# hic
a
Copy code
Missing output file(s) `*.html` expected by process `NFCORE_HIC:HIC:FASTQC (prog_iPAX7_Dox_rep3)`

Command executed:

  printf "%s %s\n" prog_iPAX7_Dox_rep3_R1.fastq.gz prog_iPAX7_Dox_rep3_1.gz prog_iPAX7_Dox_rep3_R2.fastq.gz prog_iPAX7_Dox_rep3_2.gz | while read old_name new_name; do
      [ -f "${new_name}" ] || ln -s $old_name $new_name
  done
  fastqc  --threads 6 prog_iPAX7_Dox_rep3_1.gz prog_iPAX7_Dox_rep3_2.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_HIC:HIC:FASTQC":
      fastqc: $( fastqc --version | sed -e "s/FastQC v//g" )
  END_VERSIONS

Command exit status:
  0

Command output:
  (empty)

Command error:
  WARNING: Skipping mount /opt/ohpc/pub/libs/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  Started analysis of prog_iPAX7_Dox_rep3_1.gz
  Started analysis of prog_iPAX7_Dox_rep3_2.gz
  Approx 5% complete for prog_iPAX7_Dox_rep3_1.gz
  Approx 5% complete for prog_iPAX7_Dox_rep3_2.gz
  Failed to process file prog_iPAX7_Dox_rep3_1.gz
  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.next(FastQFile.java:125)
  	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:77)
  	at java.base/java.lang.Thread.run(Thread.java:834)
  Failed to process file prog_iPAX7_Dox_rep3_2.gz
  uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Midline 'BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFB/77BF/' didn't start with '+'
  	at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:172)
  	at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)
  	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:77)
  	at java.base/java.lang.Thread.run(Thread.java:834)
im a bit confused about what this error means, sis there something wrong with the fastq? im trying to replicate a study: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150638 maybe some of the files were corrupted?
s
Yes, I would suggest redownloading the fastq files (and using a checksum for them if possible)
👍🏻 1
👍 1