[mkreitzman@xhost10 MISO-fastmiso]$ /gsc/software/linux-x86_64-centos5/python-science-2.7.1/bin/python misopy/run_events_analysis.py --compute-genes-psi /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/ /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/A08586_test.bam --output-dir /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results --read-len 100 MISO (Mixture of Isoforms model) Probabilistic analysis of RNA-Seq data to detect differential isoforms Use --help argument to view options. Loading settings from: /home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt Computing gene-level Psi for genes... - GFF index: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed - BAM: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/A08586_test.bam - Read length: 100 - Output directory: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results Mapping genes to their indexed GFF representation, using /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrHSCHR17_1 - Loading 10 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrHSCHR6_MHC_MANN - Loading 140 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr1 - Loading 2114 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr20 - Loading 534 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr21 - Loading 253 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr22 - Loading 506 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrHSCHR6_MHC_APD - Loading 82 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrHSCHR6_MHC_COX - Loading 168 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr3 - Loading 1198 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr2 - Loading 1480 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr5 - Loading 994 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr4 - Loading 876 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr7 - Loading 1067 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr6 - Loading 994 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr9 - Loading 811 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr8 - Loading 836 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrHSCHR6_MHC_DBB - Loading 157 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrHSCHR6_MHC_MCF - Loading 152 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrGL000209.1 - Loading 2 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrHSCHR4_1 - Loading 3 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrY - Loading 86 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrX - Loading 773 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr11 - Loading 1295 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr10 - Loading 835 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr13 - Loading 357 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr12 - Loading 1183 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr15 - Loading 705 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr14 - Loading 730 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr17 - Loading 919 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr16 - Loading 623 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr19 - Loading 971 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chr18 - Loading 210 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrHSCHR6_MHC_SSTO - Loading 150 genes Loading indexed gene filenames from: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/chrHSCHR6_MHC_QBL - Loading 164 genes Skipping: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/genes_to_filenames.shelve.dat Skipping: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/genes_to_filenames.shelve.dir Skipping: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/genes_to_filenames.shelve.bak Skipping: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/compressed_ids_to_genes.shelve.dat Skipping: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/compressed_ids_to_genes.shelve.dir Skipping: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/compressed_ids_to_genes.shelve.bak Skipping: /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/genes.gff Preparing to run 4 batches of jobs... Running batch of 5345 genes.. - Executing: python /projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py --compute-genes-from-file "/projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results/batch-genes/batch-0_genes.txt" /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/A08586_test.bam /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results --read-len 100 --overhang-len 1 --settings-filename /home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt - Submitted thread batch-0 Running batch of 5345 genes.. - Executing: python /projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py --compute-genes-from-file "/projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results/batch-genes/batch-1_genes.txt" /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/A08586_test.bam /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results --read-len 100 --overhang-len 1 --settings-filename /home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt - Submitted thread batch-1 Running batch of 5345 genes.. - Executing: python /projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py --compute-genes-from-file "/projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results/batch-genes/batch-2_genes.txt" /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/A08586_test.bam /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results --read-len 100 --overhang-len 1 --settings-filename /home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt - Submitted thread batch-2 Running batch of 5346 genes.. - Executing: python /projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py --compute-genes-from-file "/projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results/batch-genes/batch-3_genes.txt" /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/A08586_test.bam /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results --read-len 100 --overhang-len 1 --settings-filename /home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt - Submitted thread batch-3 Waiting on 4 threads... Traceback (most recent call last): File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 493, in main() File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 437, in main run_compute_genes_from_file(options) File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 252, in run_compute_genes_from_file event_type=options.event_type) File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 130, in compute_gene_psi gene_obj) File "/home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/misopy/sam_utils.py", line 191, in fetch_bam_reads_in_gene chrom = chrom_parts[1] IndexError: list index out of range Traceback (most recent call last): File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 493, in main() File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 437, in main run_compute_genes_from_file(options) File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 252, in run_compute_genes_from_file event_type=options.event_type) File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 130, in compute_gene_psi gene_obj) File "/home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/misopy/sam_utils.py", line 191, in fetch_bam_reads_in_gene chrom = chrom_parts[1] IndexError: list index out of range Traceback (most recent call last): File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 493, in main() File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 437, in main run_compute_genes_from_file(options) File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 252, in run_compute_genes_from_file event_type=options.event_type) File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 130, in compute_gene_psi gene_obj) File "/home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/misopy/sam_utils.py", line 191, in fetch_bam_reads_in_gene chrom = chrom_parts[1] IndexError: list index out of range Traceback (most recent call last): File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 493, in main() File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 437, in main run_compute_genes_from_file(options) File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 252, in run_compute_genes_from_file event_type=options.event_type) File "/projects/mkreitzman_prj/expression_quantification_testing/MISO-fastmiso/misopy/run_miso.py", line 130, in compute_gene_psi gene_obj) File "/home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/misopy/sam_utils.py", line 191, in fetch_bam_reads_in_gene chrom = chrom_parts[1] IndexError: list index out of range WARNING: Thread batch-0 might have failed... WARNING: Thread batch-1 might have failed... WARNING: Thread batch-2 might have failed... WARNING: Thread batch-3 might have failed... - Threads completed in 0.00 hours.