Dear developer,
I have been trying to simulate some in silico tumors using BAMSurgeon. After installing (check_dependencies.py not throwing any errors) and generating random sites using randomsites.py, I tried introducing SNVs with addsnv.py. I am running the following command
python3 -O /home/artzo/bin/bamsurgeon/bin/addsnv.py \
-v random_SNV_1k.txt \
-f [BAM FILE] \
-r [GENOME FILE] \
-o [OUTPUT FILE] \
--aligner mem \
--picardjar [PATH TO PICARD.JAR] \
--tagreads \
--seed 2010 \
-p 12 \
--insane
I redacted the file paths in the above command. I got some errors regarding sanity checks, so I decided to use --insane. The script runs for about 20 min generating temporary files and a surprisingly small output BAM. The error.log is rather lengthy (>75k lines) and ends with
INFO 2022-06-20 14:41:34,076 loading donor reads into dictionary...
INFO 2022-06-20 14:41:34,774 secondary reads count:0
INFO 2022-06-20 14:41:34,774 supplementary reads count:0
INFO 2022-06-20 14:41:34,774 loaded 229926 reads, (144 excluded, 0 null or secondary or supplementary--> ignored)
Traceback (most recent call last):
File "/home/artzo/bin/bamsurgeon/bin/addsnv.py", line 479, in <module>
run()
File "/home/artzo/bin/bamsurgeon/bin/addsnv.py", line 476, in run
main(args)
File "/home/artzo/bin/bamsurgeon/bin/addsnv.py", line 422, in main
rr.replace_reads(args.bamFileName, outbam_mutsfile, args.outBamFile, keepqual=True, seed=args.seed)
File "/lila/home/artzo/bin/bamsurgeon/bin/bamsurgeon/replace_reads.py", line 165, in replace_reads
rdict[extqname].qual = read.qual
File "pysam/calignedsegment.pyx", line 2182, in pysam.calignedsegment.AlignedSegment.qual.__get__
File "pysam/cutils.pyx", line 45, in pysam.cutils.array_to_qualitystring
AttributeError: 'array.array' object has no attribute 'tostring'
I have read that the tostring issue might be due to incompatibilities with Python 3.9 (which I am using). However, tostring was deprecated in Python 3.2 and I find it hard to believe that all other users are using Python < 3.2. So, I was wondering whether a different issue might be at play here. I would greatly appreciate your help!
Thank you very much for the development and support of BAMSurgeon!
Best,
Oliver
Dear developer,
I have been trying to simulate some in silico tumors using BAMSurgeon. After installing (
check_dependencies.pynot throwing any errors) and generating random sites usingrandomsites.py, I tried introducing SNVs withaddsnv.py. I am running the following commandI redacted the file paths in the above command. I got some errors regarding sanity checks, so I decided to use
--insane. The script runs for about 20 min generating temporary files and a surprisingly small output BAM. The error.log is rather lengthy (>75k lines) and ends withI have read that the
tostringissue might be due to incompatibilities with Python 3.9 (which I am using). However,tostringwas deprecated in Python 3.2 and I find it hard to believe that all other users are using Python < 3.2. So, I was wondering whether a different issue might be at play here. I would greatly appreciate your help!Thank you very much for the development and support of BAMSurgeon!
Best,
Oliver