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BGI-Qingdao / TGS-GapCloser

A gap-closing software tool that uses long reads to enhance genome assembly.
GNU General Public License v3.0
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Core dump #39

Closed markcharder closed 3 years ago

markcharder commented 3 years ago

I've tried running TGS GapCloser as both a conda installation and a source installation and both times I get the following error:

/data/software/miniconda2/envs/tgsgapcloser/bin/tgsgapcloser: line 374: 2187092 Aborted (core dumped) $Candidate --ont_reads_a $TGS_READS --contig2ont_paf $OUT_PREFIX.sub.paf --candidate_max 10 --candidate_shake_filter --candidate_merge < $TMP_INPUT_SCAFF_INFO > $OUT_PREFIX.ont.fasta 2> $OUT_PREFIX.cand.log

Ubuntu 20.04.2 LTS

adonis316 commented 3 years ago

Hi, Can you please provide us a few input sequences and all log files? Note that TGS-GapCloser will work only if the input scaffolds have unknown “N” sequences.

Thanks, Mengyang

markcharder commented 3 years ago

I have found that the problem was that TGS-GapCloser requires reads in fasta format but I had reads in fastq format. Sorry for the post. Closing the issue.