miso pipeline fails to run

[gpratt]

Here is the command + stack trace to repo

[gpratt@tscc-login1 ~]$ submit_miso_pipeline.py  '--bam' '/home/gpratt/projects/roche_riboseq/analysis/npc_riboseq_v1/3R21_CAGATC_L008_R1.fastq.gz.polyATrim.adapterTrim.rmRep.sorted.rg.bam'  '--sample-id' '3R21_CAGATC_L008_R1'  '--genome' 'hg19'  '--single-end'  '--output-sh' '/home/gpratt/projects/roche_riboseq/analysis/npc_riboseq_v1/3R21_CAGATC_L008_R1.fastq.gz.polyATrim.adapterTrim.rmRep.sorted.rg.miso'  && sh /home/gpratt/projects/roche_riboseq/analysis/npc_riboseq_v1/3R21_CAGATC_L008_R1.fastq.gz.polyATrim.adapterTrim.rmRep.sorted.rg.miso
Vendor:  Continuum Analytics, Inc.
Package: mkl
Message: trial mode expires in 29 days
Traceback (most recent call last):
  File "/projects/ps-yeolab/software/anaconda/bin/submit_miso_pipeline.py", line 5, in <module>
    pkg_resources.run_script('gscripts==0.1.6', 'submit_miso_pipeline.py')
  File "/projects/ps-yeolab/software/anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py", line 534, in run_script
    added to the working set.
  File "/projects/ps-yeolab/software/anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py", line 1434, in run_script
    """Provider based on a virtual filesystem"""
  File "/projects/ps-yeolab/software/anaconda/lib/python2.7/site-packages/gscripts-0.1.6-py2.7.egg/EGG-INFO/scripts/submit_miso_pipeline.py", line 314, in <module>
    main()
  File "/projects/ps-yeolab/software/anaconda/lib/python2.7/site-packages/gscripts-0.1.6-py2.7.egg/EGG-INFO/scripts/submit_miso_pipeline.py", line 280, in main
    cl.args['annotation_index_strfrmt'],
KeyError: 'annotation_index_strfrmt'

[gpratt]

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

[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

[gpratt]

Looks like its working now, didn't see that log file. Thanks!

[olgabot]

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.