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simoncchu / GAPPadder

GAPPadder is tool for closing gaps on draft genomes with short sequencing data
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merge_dispatch_reads_for_gaps_v2 step throwing "IndexError: list index out of range" #3

Closed jos4uke closed 6 years ago

jos4uke commented 6 years ago

Hi

I am currently running GAPPadder on some short reads assembly but getting this error at merge_dispatch_reads_for_gaps_v2 step

python ./GAPPadder/main.py -c All -g GAPPadder_configuration_CLC.json

Traceback (most recent call last): File "./GAPPadder/main.py", line 283, in main_func(scommand,sfconfig) File "./GAPPadder/main.py", line 257, in main_func drc.merge_dispatch_reads_for_gaps_v2(left_reads, right_reads) File "./GAPPadder/run_multi_threads_discordant.py", line 213, in merge_dispatch_reads_for_gaps_v2 temp_field=id_fields[0].split("/") IndexError: list index out of range

Any idea why this error occured?

Thanks in advance

jos4uke commented 6 years ago

I can close this issue, it was the input reads. I didn't check that GAPPadder expects only fastq and no compressed fastq.