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PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
BSD 3-Clause Clear License
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LA4Falcon faild. #105

Closed WenchaoLin closed 6 years ago

WenchaoLin commented 6 years ago

falcon_unzip faild, do you have any suggestions?

manually run /3-unzip/reads/task.sh shows error as follows:

LA4Falcon -m falcon/0-rawreads/raw_reads.db falcon/0-rawreads/m_00001/raw_reads.1.raw_reads.2.N0.las

about to go into loop with novl = 166665 falcon/0-rawreads/m_00001/raw_reads.1.raw_reads.2.N0.las
before Read_Overlap record j = 0 out of 166665 at falcon/0-rawreads/m_00001/raw_reads.1.raw_reads.2.N0.las Thu Jan 11 11:21:09 2018
Segmentation fault (core dumped)

while I run the LA4Falcon executable copied from the origin FALCON bin with the same command it shows:

LA4Falcon: Non-positive index?, '0'
pb-cdunn commented 6 years ago

Hmmm. If you could get a stack-trace for that LA4Falcon seg-fault, maybe we could help.

while I run the LA4Falcon executable copied from the origin FALCON bin

I'm not sure what that means. Any idea which commit of DALIGNER is used for each?

WenchaoLin commented 6 years ago

The assembly were using obsoleted falcon. Problem solved by update falcon to the latest version. Thanks.