Solved more or less - Ubuntu: MISO unittest fails

Question

[thefirstrealace]

Hello,

I have the following problem. I installed MISO with pip like described in the installation guide using:

$ pip install misopy

After several attempts it finally worked. I did the first testing step of the installation:

$ module_availability

Here again there were no problems. Right after that I tried to do the unittest with:

$ python -m unittest discover misopy

I tried it without root and after it failed I tried it with root and I got the following message:

root@AceExt:~# python -m unittest discover misopy
Testing fr-unstranded...
Checking read  f_read  against  +
Checking read  f_read  against  -
Checking read  r_read  against  +
Checking read  r_read  against  -
Testing fr-firststrand...
.Testing conversion of SAM to BAM...
Executing: sam_to_bam --convert /usr/local/lib/python2.7/dist-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output
Converting SAM to BAM...
  - Executing: samtools view -Sbh /usr/local/lib/python2.7/dist-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam  > /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam
[main_samview] fail to open "/usr/local/lib/python2.7/dist-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam" for reading.
Sorting BAM file...
  - Executing: samtools sort /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Segmentation fault (core dumped)
Indexing BAM...
  - Executing: samtools index /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
open: No such file or directory
[bam_index_build2] fail to open the BAM file.
Conversion took 0.00 minutes.
FTesting gene-level Psi...
Testing GFF indexing of: /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
Executing: index_gff --index /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed
Indexing GFF...
  - GFF: /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
  - Outputting to: /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed
Traceback (most recent call last):
  File "/usr/local/bin/index_gff", line 11, in <module>
    sys.exit(main())
  File "/usr/local/lib/python2.7/dist-packages/misopy/index_gff.py", line 191, in main
    compress_id=options.compress_id)
  File "/usr/local/lib/python2.7/dist-packages/misopy/index_gff.py", line 153, in index_gff
    gff_genes = gene_utils.load_genes_from_gff(gff_filename)
  File "/usr/local/lib/python2.7/dist-packages/misopy/Gene.py", line 878, in load_genes_from_gff
    reverse_recs=reverse_recs)
  File "/usr/local/lib/python2.7/dist-packages/misopy/gff_utils.py", line 191, in __init__
    include_introns=include_introns)
  File "/usr/local/lib/python2.7/dist-packages/misopy/gff_utils.py", line 201, in from_file
    FILE = open(filename, "r")
IOError: [Errno 2] No such file or directory: '/usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff'
Executing: miso --run /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /usr/local/lib/python2.7/dist-packages/misopy/test-output/gene-psi-output --read-len 36 
MISO (Mixture of Isoforms model)
Probabilistic analysis of RNA-Seq data for detecting differential isoforms
Use --help argument to view options.

Using MISO settings file: /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
Error: Settings file /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt does not exist.
.Testing gene-level Psi...
Executing: python /usr/local/lib/python2.7/dist-packages/misopy/index_gff.py --index /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/indexed
Indexing GFF...
  - GFF: /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
  - Outputting to: /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/indexed
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/misopy/index_gff.py", line 199, in <module>
    main()
  File "/usr/local/lib/python2.7/dist-packages/misopy/index_gff.py", line 191, in main
    compress_id=options.compress_id)
  File "/usr/local/lib/python2.7/dist-packages/misopy/index_gff.py", line 153, in index_gff
    gff_genes = gene_utils.load_genes_from_gff(gff_filename)
  File "/usr/local/lib/python2.7/dist-packages/misopy/Gene.py", line 878, in load_genes_from_gff
    reverse_recs=reverse_recs)
  File "/usr/local/lib/python2.7/dist-packages/misopy/gff_utils.py", line 191, in __init__
    include_introns=include_introns)
  File "/usr/local/lib/python2.7/dist-packages/misopy/gff_utils.py", line 201, in from_file
    FILE = open(filename, "r")
IOError: [Errno 2] No such file or directory: '/usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff'
Executing: python /usr/local/lib/python2.7/dist-packages/misopy/run_events_analysis.py  --compute-genes-psi /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/indexed /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /usr/local/lib/python2.7/dist-packages/misopy/test-output/gene-psi-output --read-len 36  --paired-end 250 30 --use-cluster
MISO (Mixture of Isoforms model)
To run MISO, please use "miso" instead.
.Testing single-end SE event interface...
Executing: python /usr/local/lib/python2.7/dist-packages/misopy/run_events_analysis.py  --compute-events-psi se-sample /usr/local/lib/python2.7/dist-packages/misopy/test-data/se-counts/se_test.counts --output-dir /usr/local/lib/python2.7/dist-packages/misopy/test-output/SE-output --read-len 35 --overhang-len 4  --event-type SE --use-cluster 
MISO (Mixture of Isoforms model)
To run MISO, please use "miso" instead.
.
======================================================================
FAIL: test_a_sam_to_bam (misopy.test_miso.TestMISO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/misopy/test_miso.py", line 51, in test_a_sam_to_bam
    "c2c12.Atp2b1.sorted.bam")))
AssertionError

----------------------------------------------------------------------
Ran 5 tests in 1.014s

FAILED (failures=1)

I hope that somebody can help me with that.

Best regards

Answer 1

[thefirstrealace]

I actually managed to solve the problem myself. I removed everything using

$ pip uninstall "thisandthat"

and i reinstalled MISO doing THE EXACT SAME STEPS like shown in the installation guide. For some reason it everything worked perfectly, so i guess it was just some kind of vodoo curse that you encounter every now and then when using ubuntu.

Anyway, sorry for the trouble.

[priyadhawan11234]

installed misopy by anaconda $python -m unittest discover misopy Traceback (most recent call last): File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main "__main__", fname, loader, pkg_name) File "/usr/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/usr/lib/python2.7/unittest/__main__.py", line 12, in <module> main(module=None) File "/usr/lib/python2.7/unittest/main.py", line 94, in __init__ self.parseArgs(argv) File "/usr/lib/python2.7/unittest/main.py", line 113, in parseArgs self._do_discovery(argv[2:]) File "/usr/lib/python2.7/unittest/main.py", line 214, in _do_discovery self.test = loader.discover(start_dir, pattern, top_level_dir) File "/usr/lib/python2.7/unittest/loader.py", line 204, in discover raise ImportError('Start directory is not importable: %r' % start_dir) ImportError: Start directory is not importable: 'misopy'