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biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
31 stars 6 forks source link

epic-effective cannot find jellyfish #50

Open IanCodes opened 7 years ago

IanCodes commented 7 years ago

Hi,

I have installed epic and jellyfish in a virtualenv: virtualenv venv.epic_0.1.25 . /path/venv.epic_0.1.25/bin/activate pip install bioepic pip install jellyfish

When I try to run epic-effective as: epic-effective --read-length=76 --nb-cpu=12 oviAri3_BASE.fa

I get the following error: Temporary directory: /tmp/86174.1.C6320-512-haswell.q (File: effective_genome_size, Log level: INFO, Time: Tue, 14 Mar 2017 16:40:11 ) File analyzed: oviAri3_BASE.fa (File: effective_genome_size, Log level: INFO, Time: Tue, 14 Mar 2017 16:40:11 ) Genome length: 2587507083 (File: effective_genome_size, Log level: INFO, Time: Tue, 14 Mar 2017 16:40:11 ) /bin/sh: jellyfish: command not found /bin/sh: jellyfish: command not found Traceback (most recent call last): File "/mnt/fls01-home01/user/virtualenvs/venv.epic_0.1.25/bin/epic-effective", line 38, in effective_genome_size(fasta, read_length, nb_cpu, tmpdir) File "/mnt/fls01-home01/user/virtualenvs/venv.epic_0.1.25/lib/python2.7/site-packages/epic/scripts/effective_genome_size.py", line 56, in effective_genome_size shell=True) File "/opt/gridware/depots/4baff5c5/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/subprocess.py", line 573, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command 'jellyfish stats /tmp/86174.1.C6320-512-haswell.q/oviAri3_BASE.fa.jf' returned non-zero exit status 127 rm: cannot remove ‘/tmp/86174.1.C6320-512-haswell.q/oviAri3_BASE.fa.jf’: No such file or directory

Thanks.

endrebak commented 7 years ago

Thanks for reporting this :)

Is jellyfish on your path? Try running jellyfish in your shell and see what happens.

IanCodes commented 7 years ago

The epic virtualenv is active, but when I type 'jellyfish' I get: -bash: jellyfish: command not found

But it has been installed by pip: 'pip list' shows: jellyfish (0.5.6)

endrebak commented 7 years ago

Ah, jellyfish in pip is something else. You need to get it from Bioconda or here

http://www.genome.umd.edu/jellyfish.html

Please do not close this thread. I'll use it as a reminder to update the docs when I get more time :)

Again, thanks for reporting. Totally sensible question/misunderstanding.