Anand Parikh
07/01/2024, 1:05 PMMissing 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?Simon Pearce
07/01/2024, 1:29 PM