Closed gpratt closed 10 years ago
I've got a new error now:
submit_miso_pipeline.py '--bam' '/home/gpratt/projects/encode_integration/analysis/encode_rnaseq_v1/K562_Long_Total_TruSeq_2x100_ENCLB058ZZZ_Grav.bam.sorted.rg.bam' '--sample-id' 'K562_Long_Total_TruSeq_2x100_ENCLB058ZZZ_Grav' '--genome' 'hg19' '--do-not-submit' '--output-sh' '/home/gpratt/projects/encode_integration/analysis/encode_rnaseq_v1/K562_Long_Total_TruSeq_2x100_ENCLB058ZZZ_Grav.bam.sorted.rg.miso' && sh /home/gpratt/projects/encode_integration/analysis/encode_rnaseq_v1/K562_Long_Total_TruSeq_2x100_ENCLB058ZZZ_Grav.bam.sorted.rg.miso
ERROR 11:03:52,673 FunctionEdge - Contents of /home/gpratt/projects/encode_integration/analysis/encode_rnaseq_v1/K562_Long_Total_TruSeq_2x100_ENCLB058ZZZ_Grav.bam.sorted.rg.miso.out:
discarding /projects/ps-yeolab/software/anaconda/bin from PATH
prepending /projects/ps-yeolab/software/anaconda/envs/gpratt/bin to PATH
discarding /projects/ps-yeolab/software/anaconda/bin from PATH
prepending /projects/ps-yeolab/software/anaconda/envs/gpratt/bin to PATH
/projects/ps-yeolab/software/anaconda/envs/gpratt/lib/python2.7/site-packages/pandas/io/excel.py:626: UserWarning: Installed openpyxl is not supported at this time. Use >=1.6.1 and <2.0.0.
.format(openpyxl_compat.start_ver, openpyxl_compat.stop_ver))
Wrote miso script for sample "K562_Long_Total_TruSeq_2x100_ENCLB058ZZZ_Grav": /home/gpratt/projects/encode_integration/analysis/encode_rnaseq_v1/K562_Long_Total_TruSeq_2x100_ENCLB058ZZZ_Grav.bam.sorted.rg.miso
MISO psi failed on event type: SE
Any pointers?
@olgabot
Does pip install misopy
in your environment fix it?
I see this:
(olga)[obotvinnik@tscc-login2 miso]$ less /home/gpratt/projects/encode_integration/analysis/encode_rnaseq_v1/miso/K562_Long_Total_TruSeq_2x100_ENCLB058ZZZ_Grav/SE/summary.err
Traceback (most recent call last):
File "/home/yeo-lab/software/bin/run_miso.py", line 11, in <module>
import misopy
ImportError: No module named misopy
Looks like its working now, didn't see that log file. Thanks!
no problem! in case you want to find that in the future, look in the "*.miso" file created, e.g. /home/gpratt/projects/encode_integration/analysis/encode_rnaseq_v1/K562_Long_Total_TruSeq_2x100_ENCLB058ZZZ_Grav.bam.sorted.rg.miso
for the psi.err
and summary.err
files on the splice type that it failed on. In this case, it was SE
, so that's how I found that file.
Here is the command + stack trace to repo