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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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read-correction crashes #6

Closed dominik-handler closed 4 years ago

dominik-handler commented 4 years ago

Hi, I am trying to run TGS-GapCloser with RACON read correction. I get the follwoing error message: /install/TGS-GapCloser/TGS-GapCloser.sh: line 366: 26837 Aborted $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

I am certain that it is not a memory problem as plenty should be available. Do you have any idea what can be wrong here? If required I can give you access to the folder containing the data.

Thank you, Dominik

cchd0001 commented 4 years ago

Hi Dominik, Please check your $TGS_READS , FASTQ format is not supported and always cause crash. If TGS_READS is in FSATA format , please provide me a small piece of data that can reproduce this crash so that I can debug it , thanks

Best wishes Lidong

dominik-handler commented 4 years ago

Ah, thank you for your reply. My reads are indeed FASTQ. Will try again after converting them to FASTA.

All the best, Dominik