Segmentation fault

[chunlinxiao]

For some reason, my verkko2.1 run got "Segmentation fault" at the step of "7-consensus" (please see the error below).

I checked the input sequences, and found no reads (ONT or HiFi) with special char (non ATGC) or length > 2 Mb.

DO you have any idea?

Thanks

>tail verkko2.1_out/7-consensus/buildPackages.err
-- Loading layouts - tig  33812 of length     40855 bp with      80 reads
-- Loading layouts - tig  33813 of length     41961 bp with      81 reads
-- Loading layouts - tig  33814 of length     44123 bp with      97 reads
ERROR: loading layouts failed, check your input sequences and layout file!
layoutToPackage: utgcns/layoutToPackage.C:167: void loadVerkkoLayouts(sqCache*, std::vector<tgTig*>&, merylutil::files::v1::compressedFileReader*, const char*): Assertion `0' failed.

Failed with 'Aborted'; backtrace (libbacktrace):

Failed with 'Segmentation fault'; backtrace (libbacktrace):
./buildPackages.sh: line 14: 1483220 Segmentation fault      (core dumped) ...miniconda3/envs/myconda_verkko_v2.1/lib/verkko/bin/layoutToPackage -layout ../6-layoutContigs/unitig-popped.layout -output packages/part###.cnspack -idmap packages -partition 0.8 1.5 0.04 -reads ../7-consensus/ont_subset.fasta.gz ../m84039_combined.fastq.gz > ../7-consensus/packages.report

[skoren]

This usually implies you're missing some sequences that the layouts name but then are not in your provided fasta/fastq. Have any files been moved in the filesystem during this run? Can you grep for ERROR in the full buildPackages.err file and post the results here?