Hello all, I am trying to process Capture Hi-C data produced by another lab. I have been getting this error in the pipeline: ERROR ~ Error executing process > 'NFCORE_HICHICFASTQC (REP1)' Caused by: Process

NFCORE_HIC:HIC:FASTQC (REP1)

terminated with an error exit status (1) Command executed: printf "%s %s\n" SRR25078824_GSM7519874_Wild-type_heart_CaptureHiC_rep1_Mus_musculus_Hi-C_1.fastq.gz REP1_1.gz SRR25078824_GSM7519874_Wild-type_heart_CaptureHiC_rep1_Mus_musculus_Hi-C_2.fastq.gz REP1_2.gz | while read old_name new_name; do [ -f "${new_name}" ] || ln -s $old_name $new_name done fastqc --threads 6 REP1_1.gz REP1_2.gz cat <<-END_VERSIONS > versions.yml "NFCORE_HICHICFASTQC": fastqc: $( fastqc --version | sed -e "s/FastQC v//g" ) END_VERSIONS Command exit status: 1 Command output: (empty) Command error: WARNING: Skipping mount /software/singularity-3.9.2-el8-x86_64/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container Failed to process REP1_1.gz java.io.EOFException at java.base/java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:269) at java.base/java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:259) at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:165) at java.base/java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:80) at java.base/java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:92) at uk.ac.babraham.FastQC.Utilities.MultiMemberGZIPInputStream.<init>(MultiMemberGZIPInputStream.java:37) at uk.ac.babraham.FastQC.Sequence.FastQFile.<init>(FastQFile.java:80) 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 REP1_2.gz java.io.EOFException at java.base/java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:269) at java.base/java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:259) at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStreat java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:165) at java.base/java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:80) at java.base/java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:92) at uk.ac.babraham.FastQC.Utilities.MultiMemberGZIPInputStream.<init>(MultiMemberGZIPInputStream.java:37) at uk.ac.babraham.FastQC.Sequence.FastQFile.<init>(FastQFile.java:80) 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) Tip: you can replicate the issue by changing to the process work dir and entering the command

bash .command.run

Hmm could you try skipping FASTQC? Which branch are you running?

I don't believe that skipping the fastqc step is possible for this pipeline and when I have tried this it ignores the parameter and continues to fail in the same way. This is the master branch.

Could you try running it on dev with

-r dev

? If you could also kick a run off with the

nf-validation

branch if dev doesn't get the job done.