nf-core
We're missing aa proper intervals file for GRCh37
Description of the bug
we have a .list, we should either have a .bed or a .interval_list
Command used and terminal output
No response
Relevant files
No response
System information
No response
After renaming the interval file (.list) into .bed, I got this error:
Error executing process > 'NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (wgs_calling_regions_Sarek.bed)'
Caused by:
Process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (wgs_calling_regions_Sarek.bed) terminated with an error exit status (127)
Command executed:
awk -vFS=" " '{ t = $5 # runtime estimate if (t == "") { # no runtime estimate in this row, assume default value t = ($3 - $2) / 1000 } if (name == "" || (chunk > 600 && (chunk + t) > longest * 1.05)) { # start a new chunk name = sprintf("%s_%d-%d.bed", $1, $2+1, $3) chunk = 0 longest = 0 } if (t > longest) longest = t chunk += t print $0 > name }' wgs_calling_regions_Sarek.bed
cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED": gawk: $(awk -Wversion | sed '1!d; s/.Awk //; s/,.//') END_VERSIONS
Command exit status: 127
Command output: (empty)
Command error: WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container /bin/bash: line 0: cd: /beegfs/scratch/ric.cosr/ric.cosr/B1MG/work/7b/8c58dbb4a706cd1461d6f1daa88364: No such file or directory /bin/bash: .command.run: No such file or directory
Work dir: /beegfs/scratch/ric.cosr/ric.cosr/B1MG/work/7b/8c58dbb4a706cd1461d6f1daa88364
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
It sounded a little bit strange since both the work directory and the .command.run file are there.
This should be fixed in #727 . Let me know, if you run into any more issues :)
