Error when running MISO

Question

[onspotproductions]

When I attempt to run MISO it loads all the files correctly, but when it submites the processes the threads fail. I ran the test they recommend to run and get an error, but it doesn't seem relevant as I am not converting sam to bam. I also have been trying to install numpy 1.6.2 as it gives a warning for that but installing via pip only gives 1.6.1

/Library/Python/2.7/site-packages/scipy/__init__.py:111: UserWarning: Numpy 1.6.2 or above is recommended for this version of scipy (detected version 1.6.1)
  UserWarning)
Testing gene-level Psi...
Executing: python /Library/Python/2.7/site-packages/misopy/index_gff.py --index /Library/Python/2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /Library/Python/2.7/site-packages/misopy/gff-events/mm9/indexed
/Library/Python/2.7/site-packages/scipy/__init__.py:111: UserWarning: Numpy 1.6.2 or above is recommended for this version of scipy (detected version 1.6.1)
  UserWarning)
Indexing GFF...
/Library/Python/2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff appears to already be indexed. Aborting.
Executing: python /Library/Python/2.7/site-packages/misopy/run_events_analysis.py  --compute-genes-psi /Library/Python/2.7/site-packages/misopy/gff-events/mm9/indexed /Library/Python/2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /Library/Python/2.7/site-packages/misopy/test-output/gene-psi-output --read-len 36  --paired-end 250 30 --use-cluster
/Library/Python/2.7/site-packages/scipy/__init__.py:111: UserWarning: Numpy 1.6.2 or above is recommended for this version of scipy (detected version 1.6.1)
  UserWarning)
MISO (Mixture of Isoforms model)
To run MISO, please use "miso" instead.
.Testing single-end SE event interface...
Executing: python /Library/Python/2.7/site-packages/misopy/run_events_analysis.py  --compute-events-psi se-sample /Library/Python/2.7/site-packages/misopy/test-data/se-counts/se_test.counts --output-dir /Library/Python/2.7/site-packages/misopy/test-output/SE-output --read-len 35 --overhang-len 4  --event-type SE --use-cluster 
/Library/Python/2.7/site-packages/scipy/__init__.py:111: UserWarning: Numpy 1.6.2 or above is recommended for this version of scipy (detected version 1.6.1)
  UserWarning)
MISO (Mixture of Isoforms model)
To run MISO, please use "miso" instead.
.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 /Library/Python/2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam /Library/Python/2.7/site-packages/misopy/test-output/sam-output
Converting SAM to BAM...
  - Executing: samtools view -Sbh /Library/Python/2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam  > /Library/Python/2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam
Sorting BAM file...
  - Executing: samtools sort /Library/Python/2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam /Library/Python/2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name
  -o FILE    Write final output to FILE rather than standard output
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam
  -@, --threads INT
             Set number of sorting and compression threads [1]
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
Indexing BAM...
  - Executing: samtools index /Library/Python/2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
[E::hts_open_format] fail to open file '/Library/Python/2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam'
samtools index: failed to open "/Library/Python/2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam": No such file or directory
Conversion took 0.00 minutes.
FTesting gene-level Psi...
Testing GFF indexing of: /Library/Python/2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
Executing: index_gff --index /Library/Python/2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /Library/Python/2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed
Indexing GFF...
/Library/Python/2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff appears to already be indexed. Aborting.
Executing: miso --run /Library/Python/2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed /Library/Python/2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /Library/Python/2.7/site-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/site-packages/misopy/settings/miso_settings.txt
Computing Psi values...
  - GFF index: /Library/Python/2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed
  - BAM: /Library/Python/2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
  - Read length: 36
  - Output directory: /Library/Python/2.7/site-packages/misopy/test-output/gene-psi-output
Checking your GFF annotation and BAM for mismatches...
Error: BAM /Library/Python/2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam cannot be found.
02/06/2016 05:39:49 PM - miso_main - ERROR - BAM file /Library/Python/2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam not found.
.
======================================================================
FAIL: test_a_sam_to_bam (misopy.test_miso.TestMISO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Python/2.7/site-packages/misopy/test_miso.py", line 51, in test_a_sam_to_bam
    "c2c12.Atp2b1.sorted.bam")))
AssertionError

[onspotproductions]

Was able to fix this error but I still get

Checking your GFF annotation and BAM for mismatches...
Checking if BAM has mixed read lengths...
Found reads of length 99 in BAM.
Mapping genes to their indexed GFF representation, using /Users/evanclark/Desktop/ensGene
Searching for /Users/evanclark/Desktop/ensGene/genes_to_filenames.shelve..
  - Found shelved file.
Preparing to run 3 batches of jobs...
Running batch of 7197 genes..
  - Executing: python /usr/local/lib/python2.7/site-packages/misopy/run_miso.py --compute-genes-from-file "/Users/evanclark/Desktop/output/sf2_miso/batch-genes/batch-0_genes.txt" /Users/evanclark/Desktop/SF2/SF2.bam /Users/evanclark/Desktop/output/sf2_miso --read-len 99  --paired-end 202.3 50.7 --settings-filename /usr/local/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-0
/Library/Python/2.7/site-packages/scipy/__init__.py:111: UserWarning: Numpy 1.6.2 or above is recommended for this version of scipy (detected version 1.6.1)
  UserWarning)
Running batch of 7197 genes..
  - Executing: python /usr/local/lib/python2.7/site-packages/misopy/run_miso.py --compute-genes-from-file "/Users/evanclark/Desktop/output/sf2_miso/batch-genes/batch-1_genes.txt" /Users/evanclark/Desktop/SF2/SF2.bam /Users/evanclark/Desktop/output/sf2_miso --read-len 99  --paired-end 202.3 50.7 --settings-filename /usr/local/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-1
/Library/Python/2.7/site-packages/scipy/__init__.py:111: UserWarning: Numpy 1.6.2 or above is recommended for this version of scipy (detected version 1.6.1)
  UserWarning)
Running batch of 7197 genes..
  - Executing: python /usr/local/lib/python2.7/site-packages/misopy/run_miso.py --compute-genes-from-file "/Users/evanclark/Desktop/output/sf2_miso/batch-genes/batch-2_genes.txt" /Users/evanclark/Desktop/SF2/SF2.bam /Users/evanclark/Desktop/output/sf2_miso --read-len 99  --paired-end 202.3 50.7 --settings-filename /usr/local/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-2
/Library/Python/2.7/site-packages/scipy/__init__.py:111: UserWarning: Numpy 1.6.2 or above is recommended for this version of scipy (detected version 1.6.1)
  UserWarning)
Waiting on 3 threads...
02/07/2016 08:53:14 AM - miso_main - WARNING - Thread batch-0 might have failed...
02/07/2016 08:53:14 AM - miso_main - WARNING - Thread batch-1 might have failed...
02/07/2016 08:53:14 AM - miso_main - WARNING - Thread batch-2 might have failed.