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Israel Gonzalez
Sep 26, 2024, 11:06:14 AM9/26/24
to Biociphers
Why do I receive this error in Vola after using minreads and minpos as 1?
This is the log for all three instructions:
root@8cffbe7b52ee:/tmp# majiq build \
-o /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build \
-c /mnt/experiments/Bebee-2015-Esrps/majiq/normal/settings.ini \
/mnt/genome/gencode.vM34.primary_assembly.annotation.gff3.gz \
-j 12 --min-experiments 1 --minreads 1 --minpos 1
2024-09-26 14:30:34,801 (PID:7) - INFO - Majiq Build v2.5.7.dev1+g8ff62a93
2024-09-26 14:30:34,825 (PID:7) - INFO - Command: /usr/local/bin/majiq build -o /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build -c /mnt/experiments/Bebee-2015-Esrps/majiq/normal/settings.ini /mnt/genome/gencode.vM34.primary_assembly.annotation.gff3.gz -j 12 --min-experiments 1 --minreads 1 --minpos 1
2024-09-26 14:30:34,857 (PID:7) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-09-26 14:30:34,858 (PID:7) - INFO - ╠╡ ACADEMIC License applied ║
2024-09-26 14:30:34,858 (PID:7) - INFO - ║ Name: Official Majiq Academic-only License ║
2024-09-26 14:30:34,858 (PID:7) - INFO - ║ File: majiq_license.lic ║
2024-09-26 14:30:34,858 (PID:7) - INFO - ║ Expiration Date: Never ║
2024-09-26 14:30:34,859 (PID:7) - INFO - ║ ║
2024-09-26 14:30:34,859 (PID:7) - INFO - ╠╡ The academic license is for non-commercial purposes by ║
2024-09-26 14:30:34,859 (PID:7) - INFO - ╠╡ individuals at an academic or not for profit institution. ║
2024-09-26 14:30:34,859 (PID:7) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-09-26 14:30:35,105 (PID:7) - INFO - Parsing GFF3
2024-09-26 14:30:52,837 (PID:7) - INFO - Adding Transcript Exons
2024-09-26 14:31:14,730 (PID:7) - INFO - Reading bamfiles
2024-09-26 14:31:14,732 (PID:7) - INFO - Group A, number of experiments: 2, minexperiments: 1
2024-09-26 14:31:14,733 (PID:7) - INFO - Reading bam file /mnt/experiments/Bebee-2015-Esrps/data/bam//SRR1725976_Aligned.sortedByCoord.out.bam
2024-09-26 14:31:56,640 (PID:7) - INFO - Detect Intron retention SRR1725976_Aligned.sortedByCoord.out
2024-09-26 14:32:17,959 (PID:7) - INFO - Done Reading file SRR1725976_Aligned.sortedByCoord.out
2024-09-26 14:32:19,174 (PID:7) - INFO - Reading bam file /mnt/experiments/Bebee-2015-Esrps/data/bam//SRR1725977_Aligned.sortedByCoord.out.bam
2024-09-26 14:33:18,132 (PID:7) - INFO - Detect Intron retention SRR1725977_Aligned.sortedByCoord.out
2024-09-26 14:33:49,417 (PID:7) - INFO - Done Reading file SRR1725977_Aligned.sortedByCoord.out
2024-09-26 14:33:50,695 (PID:7) - INFO - Group B, number of experiments: 2, minexperiments: 1
2024-09-26 14:33:50,721 (PID:7) - INFO - Reading bam file /mnt/experiments/Bebee-2015-Esrps/data/bam//SRR1725983_Aligned.sortedByCoord.out.bam
2024-09-26 14:34:39,710 (PID:7) - INFO - Detect Intron retention SRR1725983_Aligned.sortedByCoord.out
2024-09-26 14:35:04,007 (PID:7) - INFO - Done Reading file SRR1725983_Aligned.sortedByCoord.out
2024-09-26 14:35:05,922 (PID:7) - INFO - Reading bam file /mnt/experiments/Bebee-2015-Esrps/data/bam//SRR1725984_Aligned.sortedByCoord.out.bam
2024-09-26 14:36:42,000 (PID:7) - INFO - Detect Intron retention SRR1725984_Aligned.sortedByCoord.out
2024-09-26 14:37:26,141 (PID:7) - INFO - Done Reading file SRR1725984_Aligned.sortedByCoord.out
2024-09-26 14:37:27,852 (PID:7) - INFO - Detecting LSVs ngenes: 57180
2024-09-26 14:40:44,924 (PID:7) - INFO - 92463 LSV found
2024-09-26 14:40:44,936 (PID:7) - INFO - DUMP file b'SRR1725976_Aligned.sortedByCoord.out'
2024-09-26 14:41:19,826 (PID:7) - INFO - Create majiq file
2024-09-26 14:41:21,925 (PID:7) - INFO - Dump majiq file
2024-09-26 14:41:23,017 (PID:7) - INFO - SRR1725976_Aligned.sortedByCoord.out: 63731 LSVs
2024-09-26 14:41:23,032 (PID:7) - INFO - DUMP file b'SRR1725977_Aligned.sortedByCoord.out'
2024-09-26 14:41:51,474 (PID:7) - INFO - Create majiq file
2024-09-26 14:41:53,623 (PID:7) - INFO - Dump majiq file
2024-09-26 14:41:54,906 (PID:7) - INFO - SRR1725977_Aligned.sortedByCoord.out: 63731 LSVs
2024-09-26 14:41:54,922 (PID:7) - INFO - DUMP file b'SRR1725983_Aligned.sortedByCoord.out'
2024-09-26 14:42:38,789 (PID:7) - INFO - Create majiq file
2024-09-26 14:42:40,913 (PID:7) - INFO - Dump majiq file
2024-09-26 14:42:42,215 (PID:7) - INFO - SRR1725983_Aligned.sortedByCoord.out: 63731 LSVs
2024-09-26 14:42:42,231 (PID:7) - INFO - DUMP file b'SRR1725984_Aligned.sortedByCoord.out'
2024-09-26 14:43:21,087 (PID:7) - INFO - Create majiq file
2024-09-26 14:43:23,492 (PID:7) - INFO - Dump majiq file
2024-09-26 14:43:25,464 (PID:7) - INFO - SRR1725984_Aligned.sortedByCoord.out: 63731 LSVs
2024-09-26 14:43:26,693 (PID:7) - INFO - MAJIQ Builder is ended successfully!
root@8cffbe7b52ee:/tmp# majiq heterogen -o /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/ -n A B \
-grp1 /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR17259{76,77}*.majiq \
-grp2 /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR17259{83,84}*.majiq \
--minreads 1 --minpos 1
2024-09-26 14:45:29,815 (PID:198) - INFO - Majiq deltapsi heterogeneous v2.5.7.dev1+g8ff62a93
2024-09-26 14:45:29,839 (PID:198) - INFO - Command: /usr/local/bin/majiq heterogen -o /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/ -n A B -grp1 /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725976_Aligned.sortedByCoord.out.majiq /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725977_Aligned.sortedByCoord.out.majiq -grp2 /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725983_Aligned.sortedByCoord.out.majiq /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725984_Aligned.sortedByCoord.out.majiq --minreads 1 --minpos 1
2024-09-26 14:45:29,860 (PID:198) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-09-26 14:45:29,860 (PID:198) - INFO - ╠╡ ACADEMIC License applied ║
2024-09-26 14:45:29,861 (PID:198) - INFO - ║ Name: Official Majiq Academic-only License ║
2024-09-26 14:45:29,861 (PID:198) - INFO - ║ File: majiq_license.lic ║
2024-09-26 14:45:29,861 (PID:198) - INFO - ║ Expiration Date: Never ║
2024-09-26 14:45:29,861 (PID:198) - INFO - ║ ║
2024-09-26 14:45:29,862 (PID:198) - INFO - ╠╡ The academic license is for non-commercial purposes by ║
2024-09-26 14:45:29,862 (PID:198) - INFO - ╠╡ individuals at an academic or not for profit institution. ║
2024-09-26 14:45:29,862 (PID:198) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-09-26 14:45:29,862 (PID:198) - INFO - GROUP1: ['/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725976_Aligned.sortedByCoord.out.majiq', '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725977_Aligned.sortedByCoord.out.majiq']
2024-09-26 14:45:29,863 (PID:198) - INFO - GROUP2: ['/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725983_Aligned.sortedByCoord.out.majiq', '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725984_Aligned.sortedByCoord.out.majiq']
2024-09-26 14:45:29,863 (PID:198) - INFO - Parsing file: /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725976_Aligned.sortedByCoord.out.majiq
2024-09-26 14:45:30,759 (PID:198) - INFO - Parsing file: /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725977_Aligned.sortedByCoord.out.majiq
2024-09-26 14:45:31,708 (PID:198) - INFO - Group A: 60980 LSVs
2024-09-26 14:45:31,708 (PID:198) - INFO - Parsing file: /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725983_Aligned.sortedByCoord.out.majiq
2024-09-26 14:45:32,742 (PID:198) - INFO - Parsing file: /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725984_Aligned.sortedByCoord.out.majiq
2024-09-26 14:45:33,714 (PID:198) - INFO - Group B: 60980 LSVs
2024-09-26 14:45:33,722 (PID:198) - INFO - Number quantifiable LSVs: 59365
2024-09-26 14:45:33,858 (PID:198) - INFO - Sampling from PSI
2024-09-26 14:45:33,881 (PID:198) - INFO - Group A performing at least 1251 psi samples per experiment to bound visualization error
2024-09-26 14:45:33,882 (PID:198) - INFO - (group 1/2, experiment 1/2) Group A sampling PSI from '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725976_Aligned.sortedByCoord.out.majiq'
2024-09-26 14:45:40,707 (PID:198) - INFO - (group 1/2, experiment 2/2) Group A sampling PSI from '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725977_Aligned.sortedByCoord.out.majiq'
2024-09-26 14:45:48,235 (PID:198) - INFO - Group B performing at least 1251 psi samples per experiment to bound visualization error
2024-09-26 14:45:48,242 (PID:198) - INFO - (group 2/2, experiment 1/2) Group B sampling PSI from '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725983_Aligned.sortedByCoord.out.majiq'
2024-09-26 14:45:55,830 (PID:198) - INFO - (group 2/2, experiment 2/2) Group B sampling PSI from '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725984_Aligned.sortedByCoord.out.majiq'
2024-09-26 14:46:04,193 (PID:198) - INFO - Store Voila LSV information
2024-09-26 14:48:28,992 (PID:198) - INFO - Calculating statistics pvalues
2024-09-26 14:48:29,019 (PID:198) - INFO - Using statistics: TNOM TTEST WILCOXON
2024-09-26 14:48:29,019 (PID:198) - INFO - Comparison: {'A': 2, 'B': 2}
2024-09-26 14:49:21,753 (PID:198) - INFO - Storing Voila file statistics
2024-09-26 14:52:07,784 (PID:198) - INFO - Majiq Heterogeneous calculation for A-B ended successfully! Result can be found at /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/
root@8cffbe7b52ee:/tmp# voila tsv \
/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/splicegraph.sql /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/*.het.voila \
--show-all \
-f /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/voila_tsv/all-pairs-het.tsv
2024-09-26 14:54:34,552 (PID:225) - INFO - Command: /usr/local/bin/voila tsv /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/splicegraph.sql /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/A-B.het.voila /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/KO-WT.het.voila --show-all -f /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/voila_tsv/all-pairs-het.tsv
2024-09-26 14:54:34,552 (PID:225) - INFO - Voila v2.5.7.dev1+g8ff62a93
2024-09-26 14:54:34,563 (PID:225) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-09-26 14:54:34,563 (PID:225) - INFO - ╠╡ ACADEMIC License applied ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ║ Name: Official Majiq Academic-only License ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ║ File: majiq_license.lic ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ║ Expiration Date: Never ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ║ ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ╠╡ The academic license is for non-commercial purposes by ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ╠╡ individuals at an academic or not for profit institution. ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-09-26 14:54:34,563 (PID:225) - INFO - config file: /tmp/tmpdvwnnh95
2024-09-26 14:54:34,661 (PID:225) - INFO - heterogen TSV
2024-09-26 14:54:34,662 (PID:225) - INFO - Showing all results and ignoring all filters.
2024-09-26 14:54:34,716 (PID:225) - INFO - Creating Tab-delimited output file
2024-09-26 15:01:08,952 (PID:225) - ERROR - could not broadcast input array from shape (4,) into shape (5,)
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/local/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 569, in tsv_row
for grp, medians in zip(group_names, het.median_psi):
File "/usr/local/lib/python3.10/site-packages/rna_voila/api/view_matrix.py", line 737, in median_psi
return self._median_psi()
File "/usr/local/lib/python3.10/site-packages/rna_voila/api/view_matrix.py", line 770, in _median_psi
median_psi[idx, :] = medians[:, ndx] # fill median_psi
ValueError: could not broadcast input array from shape (4,) into shape (5,)
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.10/site-packages/rna_voila/run_voila.py", line 515, in main
args.func()
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 88, in __init__
HeterogenTsv()
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 453, in __init__
super().__init__(ViewHeterogens)
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 122, in __init__
self.tab_output()
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 509, in tab_output
self.write_tsv(fieldnames)
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 335, in write_tsv
[r.get() for r in multiple_results]
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 335, in <listcomp>
[r.get() for r in multiple_results]
File "/usr/local/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
ValueError: could not broadcast input array from shape (4,) into shape (5,)
-o /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build \
-c /mnt/experiments/Bebee-2015-Esrps/majiq/normal/settings.ini \
/mnt/genome/gencode.vM34.primary_assembly.annotation.gff3.gz \
-j 12 --min-experiments 1 --minreads 1 --minpos 1
2024-09-26 14:30:34,801 (PID:7) - INFO - Majiq Build v2.5.7.dev1+g8ff62a93
2024-09-26 14:30:34,825 (PID:7) - INFO - Command: /usr/local/bin/majiq build -o /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build -c /mnt/experiments/Bebee-2015-Esrps/majiq/normal/settings.ini /mnt/genome/gencode.vM34.primary_assembly.annotation.gff3.gz -j 12 --min-experiments 1 --minreads 1 --minpos 1
2024-09-26 14:30:34,857 (PID:7) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-09-26 14:30:34,858 (PID:7) - INFO - ╠╡ ACADEMIC License applied ║
2024-09-26 14:30:34,858 (PID:7) - INFO - ║ Name: Official Majiq Academic-only License ║
2024-09-26 14:30:34,858 (PID:7) - INFO - ║ File: majiq_license.lic ║
2024-09-26 14:30:34,858 (PID:7) - INFO - ║ Expiration Date: Never ║
2024-09-26 14:30:34,859 (PID:7) - INFO - ║ ║
2024-09-26 14:30:34,859 (PID:7) - INFO - ╠╡ The academic license is for non-commercial purposes by ║
2024-09-26 14:30:34,859 (PID:7) - INFO - ╠╡ individuals at an academic or not for profit institution. ║
2024-09-26 14:30:34,859 (PID:7) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-09-26 14:30:35,105 (PID:7) - INFO - Parsing GFF3
2024-09-26 14:30:52,837 (PID:7) - INFO - Adding Transcript Exons
2024-09-26 14:31:14,730 (PID:7) - INFO - Reading bamfiles
2024-09-26 14:31:14,732 (PID:7) - INFO - Group A, number of experiments: 2, minexperiments: 1
2024-09-26 14:31:14,733 (PID:7) - INFO - Reading bam file /mnt/experiments/Bebee-2015-Esrps/data/bam//SRR1725976_Aligned.sortedByCoord.out.bam
2024-09-26 14:31:56,640 (PID:7) - INFO - Detect Intron retention SRR1725976_Aligned.sortedByCoord.out
2024-09-26 14:32:17,959 (PID:7) - INFO - Done Reading file SRR1725976_Aligned.sortedByCoord.out
2024-09-26 14:32:19,174 (PID:7) - INFO - Reading bam file /mnt/experiments/Bebee-2015-Esrps/data/bam//SRR1725977_Aligned.sortedByCoord.out.bam
2024-09-26 14:33:18,132 (PID:7) - INFO - Detect Intron retention SRR1725977_Aligned.sortedByCoord.out
2024-09-26 14:33:49,417 (PID:7) - INFO - Done Reading file SRR1725977_Aligned.sortedByCoord.out
2024-09-26 14:33:50,695 (PID:7) - INFO - Group B, number of experiments: 2, minexperiments: 1
2024-09-26 14:33:50,721 (PID:7) - INFO - Reading bam file /mnt/experiments/Bebee-2015-Esrps/data/bam//SRR1725983_Aligned.sortedByCoord.out.bam
2024-09-26 14:34:39,710 (PID:7) - INFO - Detect Intron retention SRR1725983_Aligned.sortedByCoord.out
2024-09-26 14:35:04,007 (PID:7) - INFO - Done Reading file SRR1725983_Aligned.sortedByCoord.out
2024-09-26 14:35:05,922 (PID:7) - INFO - Reading bam file /mnt/experiments/Bebee-2015-Esrps/data/bam//SRR1725984_Aligned.sortedByCoord.out.bam
2024-09-26 14:36:42,000 (PID:7) - INFO - Detect Intron retention SRR1725984_Aligned.sortedByCoord.out
2024-09-26 14:37:26,141 (PID:7) - INFO - Done Reading file SRR1725984_Aligned.sortedByCoord.out
2024-09-26 14:37:27,852 (PID:7) - INFO - Detecting LSVs ngenes: 57180
2024-09-26 14:40:44,924 (PID:7) - INFO - 92463 LSV found
2024-09-26 14:40:44,936 (PID:7) - INFO - DUMP file b'SRR1725976_Aligned.sortedByCoord.out'
2024-09-26 14:41:19,826 (PID:7) - INFO - Create majiq file
2024-09-26 14:41:21,925 (PID:7) - INFO - Dump majiq file
2024-09-26 14:41:23,017 (PID:7) - INFO - SRR1725976_Aligned.sortedByCoord.out: 63731 LSVs
2024-09-26 14:41:23,032 (PID:7) - INFO - DUMP file b'SRR1725977_Aligned.sortedByCoord.out'
2024-09-26 14:41:51,474 (PID:7) - INFO - Create majiq file
2024-09-26 14:41:53,623 (PID:7) - INFO - Dump majiq file
2024-09-26 14:41:54,906 (PID:7) - INFO - SRR1725977_Aligned.sortedByCoord.out: 63731 LSVs
2024-09-26 14:41:54,922 (PID:7) - INFO - DUMP file b'SRR1725983_Aligned.sortedByCoord.out'
2024-09-26 14:42:38,789 (PID:7) - INFO - Create majiq file
2024-09-26 14:42:40,913 (PID:7) - INFO - Dump majiq file
2024-09-26 14:42:42,215 (PID:7) - INFO - SRR1725983_Aligned.sortedByCoord.out: 63731 LSVs
2024-09-26 14:42:42,231 (PID:7) - INFO - DUMP file b'SRR1725984_Aligned.sortedByCoord.out'
2024-09-26 14:43:21,087 (PID:7) - INFO - Create majiq file
2024-09-26 14:43:23,492 (PID:7) - INFO - Dump majiq file
2024-09-26 14:43:25,464 (PID:7) - INFO - SRR1725984_Aligned.sortedByCoord.out: 63731 LSVs
2024-09-26 14:43:26,693 (PID:7) - INFO - MAJIQ Builder is ended successfully!
root@8cffbe7b52ee:/tmp# majiq heterogen -o /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/ -n A B \
-grp1 /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR17259{76,77}*.majiq \
-grp2 /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR17259{83,84}*.majiq \
--minreads 1 --minpos 1
2024-09-26 14:45:29,815 (PID:198) - INFO - Majiq deltapsi heterogeneous v2.5.7.dev1+g8ff62a93
2024-09-26 14:45:29,839 (PID:198) - INFO - Command: /usr/local/bin/majiq heterogen -o /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/ -n A B -grp1 /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725976_Aligned.sortedByCoord.out.majiq /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725977_Aligned.sortedByCoord.out.majiq -grp2 /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725983_Aligned.sortedByCoord.out.majiq /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725984_Aligned.sortedByCoord.out.majiq --minreads 1 --minpos 1
2024-09-26 14:45:29,860 (PID:198) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-09-26 14:45:29,860 (PID:198) - INFO - ╠╡ ACADEMIC License applied ║
2024-09-26 14:45:29,861 (PID:198) - INFO - ║ Name: Official Majiq Academic-only License ║
2024-09-26 14:45:29,861 (PID:198) - INFO - ║ File: majiq_license.lic ║
2024-09-26 14:45:29,861 (PID:198) - INFO - ║ Expiration Date: Never ║
2024-09-26 14:45:29,861 (PID:198) - INFO - ║ ║
2024-09-26 14:45:29,862 (PID:198) - INFO - ╠╡ The academic license is for non-commercial purposes by ║
2024-09-26 14:45:29,862 (PID:198) - INFO - ╠╡ individuals at an academic or not for profit institution. ║
2024-09-26 14:45:29,862 (PID:198) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-09-26 14:45:29,862 (PID:198) - INFO - GROUP1: ['/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725976_Aligned.sortedByCoord.out.majiq', '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725977_Aligned.sortedByCoord.out.majiq']
2024-09-26 14:45:29,863 (PID:198) - INFO - GROUP2: ['/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725983_Aligned.sortedByCoord.out.majiq', '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725984_Aligned.sortedByCoord.out.majiq']
2024-09-26 14:45:29,863 (PID:198) - INFO - Parsing file: /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725976_Aligned.sortedByCoord.out.majiq
2024-09-26 14:45:30,759 (PID:198) - INFO - Parsing file: /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725977_Aligned.sortedByCoord.out.majiq
2024-09-26 14:45:31,708 (PID:198) - INFO - Group A: 60980 LSVs
2024-09-26 14:45:31,708 (PID:198) - INFO - Parsing file: /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725983_Aligned.sortedByCoord.out.majiq
2024-09-26 14:45:32,742 (PID:198) - INFO - Parsing file: /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725984_Aligned.sortedByCoord.out.majiq
2024-09-26 14:45:33,714 (PID:198) - INFO - Group B: 60980 LSVs
2024-09-26 14:45:33,722 (PID:198) - INFO - Number quantifiable LSVs: 59365
2024-09-26 14:45:33,858 (PID:198) - INFO - Sampling from PSI
2024-09-26 14:45:33,881 (PID:198) - INFO - Group A performing at least 1251 psi samples per experiment to bound visualization error
2024-09-26 14:45:33,882 (PID:198) - INFO - (group 1/2, experiment 1/2) Group A sampling PSI from '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725976_Aligned.sortedByCoord.out.majiq'
2024-09-26 14:45:40,707 (PID:198) - INFO - (group 1/2, experiment 2/2) Group A sampling PSI from '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725977_Aligned.sortedByCoord.out.majiq'
2024-09-26 14:45:48,235 (PID:198) - INFO - Group B performing at least 1251 psi samples per experiment to bound visualization error
2024-09-26 14:45:48,242 (PID:198) - INFO - (group 2/2, experiment 1/2) Group B sampling PSI from '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725983_Aligned.sortedByCoord.out.majiq'
2024-09-26 14:45:55,830 (PID:198) - INFO - (group 2/2, experiment 2/2) Group B sampling PSI from '/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/SRR1725984_Aligned.sortedByCoord.out.majiq'
2024-09-26 14:46:04,193 (PID:198) - INFO - Store Voila LSV information
2024-09-26 14:48:28,992 (PID:198) - INFO - Calculating statistics pvalues
2024-09-26 14:48:29,019 (PID:198) - INFO - Using statistics: TNOM TTEST WILCOXON
2024-09-26 14:48:29,019 (PID:198) - INFO - Comparison: {'A': 2, 'B': 2}
2024-09-26 14:49:21,753 (PID:198) - INFO - Storing Voila file statistics
2024-09-26 14:52:07,784 (PID:198) - INFO - Majiq Heterogeneous calculation for A-B ended successfully! Result can be found at /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/
root@8cffbe7b52ee:/tmp# voila tsv \
/mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/splicegraph.sql /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/*.het.voila \
--show-all \
-f /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/voila_tsv/all-pairs-het.tsv
2024-09-26 14:54:34,552 (PID:225) - INFO - Command: /usr/local/bin/voila tsv /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/build/splicegraph.sql /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/A-B.het.voila /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/heterogen/KO-WT.het.voila --show-all -f /mnt/experiments/Bebee-2015-Esrps/majiq/normal/output/voila_tsv/all-pairs-het.tsv
2024-09-26 14:54:34,552 (PID:225) - INFO - Voila v2.5.7.dev1+g8ff62a93
2024-09-26 14:54:34,563 (PID:225) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-09-26 14:54:34,563 (PID:225) - INFO - ╠╡ ACADEMIC License applied ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ║ Name: Official Majiq Academic-only License ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ║ File: majiq_license.lic ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ║ Expiration Date: Never ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ║ ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ╠╡ The academic license is for non-commercial purposes by ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ╠╡ individuals at an academic or not for profit institution. ║
2024-09-26 14:54:34,563 (PID:225) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-09-26 14:54:34,563 (PID:225) - INFO - config file: /tmp/tmpdvwnnh95
2024-09-26 14:54:34,661 (PID:225) - INFO - heterogen TSV
2024-09-26 14:54:34,662 (PID:225) - INFO - Showing all results and ignoring all filters.
2024-09-26 14:54:34,716 (PID:225) - INFO - Creating Tab-delimited output file
2024-09-26 15:01:08,952 (PID:225) - ERROR - could not broadcast input array from shape (4,) into shape (5,)
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/local/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 569, in tsv_row
for grp, medians in zip(group_names, het.median_psi):
File "/usr/local/lib/python3.10/site-packages/rna_voila/api/view_matrix.py", line 737, in median_psi
return self._median_psi()
File "/usr/local/lib/python3.10/site-packages/rna_voila/api/view_matrix.py", line 770, in _median_psi
median_psi[idx, :] = medians[:, ndx] # fill median_psi
ValueError: could not broadcast input array from shape (4,) into shape (5,)
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.10/site-packages/rna_voila/run_voila.py", line 515, in main
args.func()
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 88, in __init__
HeterogenTsv()
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 453, in __init__
super().__init__(ViewHeterogens)
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 122, in __init__
self.tab_output()
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 509, in tab_output
self.write_tsv(fieldnames)
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 335, in write_tsv
[r.get() for r in multiple_results]
File "/usr/local/lib/python3.10/site-packages/rna_voila/tsv.py", line 335, in <listcomp>
[r.get() for r in multiple_results]
File "/usr/local/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
ValueError: could not broadcast input array from shape (4,) into shape (5,)
Israel Gonzalez
Sep 26, 2024, 6:29:11 PM9/26/24
to Biociphers
I want to mention that I have make some variations of the parameters (for example, using --minreads 1, -- permissive, --markstacks -1) and this error only happens when I add --minpos 1
San Jewell
Sep 30, 2024, 10:37:40 AM9/30/24
to Biociphers
Hello,
This is a new issue, which I've not come across before. I'm going to try to reproduce it with my own data and see if I can find the issue, if not, I may need to ask to get a partial dataset from you.
Thank you very much for reporting it.
-San
San Jewell
Sep 30, 2024, 11:35:04 AM9/30/24
to Biociphers
Hi,
This morning I have tried with some test data to try to reproduce this error using the same arguments that you have and I wasn't able to do so. Would you be opposed to sharing all or part of the BAM files / annotation that you used as input so that I can try to see if there is some kind of edge case in the data that is causing this for you?
Thanks,
-San
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