search

PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
BSD 3-Clause Clear License
30 stars 18 forks source link

falcon_unzip breaks down when running blasr #77

Open yilunhuangyue opened 7 years ago

yilunhuangyue commented 7 years ago

hello, I met an error when running falcon_unzip, It seems the pipe stopped when running blasr, there was just tmp_aln.bam.tmp in /3-unzip/0-phasing/000000F/blasr, the last lines of stderr shows as follows:

[INFO] 2017-03-30T11:33:05 [blasr] started. Warning: When attempting to select equivalently scoring reads at random the bestn parameter should be greater than one. touch /home02/wuguizhi/JLX/Falcon_test3/3-unzip/0-phasing/000000F/blasr/aln_000000F_done.exit ++ touch /home02/wuguizhi/JLX/Falcon_test3/3-unzip/0-phasing/000000F/blasr/aln_000000F_done.exit

the blasr version is 5.3.f8bfa9c.

I don not know what is the problem.

Thanks a lot for any help.

pb-cdunn commented 7 years ago

I don't think this is a version issue. We'll need your help to debug this. You can cd into the task directory and repeat just this task. There are shell scripts which show sub-shells. Hopefully you can learn something from there.

yilunhuangyue commented 7 years ago

Sorry for the late reply. It seems that the error was happened because I did not import the libraries of blasr. (error while loading shared libraries: libpbihdf.so: cannot open shared object file: No such file or directory). The blasr I used was installed by pitchfork, after export the libraries, the blasr is running now. I will send the message if I meet other errors. Thanks again for you reply.