Hi,
I have problems running majiq build.
My code:
majiq build /home/annotation/ensembl.hg19.gff3 \
-c /home/majiq/confifile.txt \
-j 4 \
-o /home/majic/build
and my confifile.txt is:
[info]
readlen=100
bamdirs=~/home/BAM_output/
genome=hg19
standness=None
[experiment]
ref_samples=control_1Aligned.sortedByCoord.out,control_2Aligned.sortedByCoord.out,control_3Aligned.sortedByCoord.out
liver=liver_1Aligned.sortedByCoord.out,liver_2Aligned.sortedByCoord.out,liver_3Aligned.sortedByCoord.out
The output of majiq is:
/home/env/lib/python3.7/site-packages/majiq/src/config.py:82: UserWarning: sjdirs parameter not found in config file, using "./" instead
'sjdirs parameter not found in config file, using "./" instead'
/home/env/lib/python3.7/site-packages/majiq/src/config.py:90: UserWarning: "readlen" parameter is deprecated and will not be used. MAJIQ now detects the maximum read length of each experiment automatically.
'"readlen" parameter is deprecated and will not be used.'
2021-04-27 13:17:24,123 (PID:3522805) - INFO - Majiq Build v2.2-e25c4ac
2021-04-27 13:17:24,124 (PID:3522805) - INFO - Command: /home/env/bin/majiq build /home/annotation/ensembl.hg19.gff3 -c /home/majic/confifile.txt -j 12 -o /home/majic/build
2021-04-27 13:17:24,124 (PID:3522805) - INFO - Parsing GFF3
2021-04-27 13:17:52,036 (PID:3522805) - INFO - Reading bamfiles
2021-04-27 13:17:52,038 (PID:3522805) - INFO - Detecting LSVs ngenes: 57773
2021-04-27 13:18:47,572 (PID:3522805) - INFO - 0 LSV found
2021-04-27 13:18:49,938 (PID:3522805) - INFO - MAJIQ Builder is ended successfully!
moreover, I'm doing something wrong and I can't find the error, because 0 LSV found doesn't make sense. I can't find my mistake.
If it useful, I run STAR with the following parameters:
--alignEndsType EndToEnd
--chimSegmentMin 2
--outFilterMismatchNmax 3
--alignIntronMax 299999
All the BAM files are sorted and indexed (.bai file)