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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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FC_Quiver Fail to open file #88

Closed AfterRain closed 7 years ago

AfterRain commented 7 years ago

Dear Developer,

I made 50X coverage DNA Samples and ran Falcon and Falcon-Unzip. However, It is failed last "fc_quiver.py" step.

It shows below error message,

samfile_fn:'./4-quiver/reads/004833F.bam' samfile_fn:'./4-quiver/reads/001125F.bam' [E::hts_open_format] fail to open file './4-quiver/reads/001125F.bam' track_reads_h.sh: line 8: 5096 Segmentation fault (core dumped) fc_select_reads_from_bam.py /shared/sample/input_bam.fofn touch /shared/sample/4-quiver/reads/track_reads_h_done.exit

There is no file "001125F.bam" in the ./4-quiver/reads folder.

Could you tell me how I trouble shoot and take look deeper?

Sincerely,

AfterRain commented 7 years ago

I solved the issue, It is happening because of file limitation. After I increased open file limit, It seems working fine.

Thank you,