tiddit_variant error #106
Description
I used small .bam files to call SVs but the process is aborted everytime. (I have been succeeded for just once). Last time I used Manta's example .bam & reference.fasta files (https://github.com/Illumina/manta/tree/master/src/demo/data) to do it, I received the error that I mention below. On the other hand, I should add that I used the TIDDIT-3.6.0 version. How can we solve this problem, or what is the reason of that issue, could you please enlighten me?
Run Code
$ tiddit --sv --bam /Users/islekbro/Desktop/SV/bams/hg19/MANTA/G15512.HCC1954.1.COST16011_region.bam -o /Users/islekbro/Desktop/SV/deneme3/manta_out --ref /Users/islekbro/Desktop/SV/genomes/manta.fa --fermi2 /Users/islekbro/miniconda3/bin/fermi2 --ropebwt2 /Users/islekbro/miniconda3/bin/ropebwt2
Error
LIBRARY STATISTICS
Pair orientation = Forward-Reverse
Average Read length = 101.0
Average insert size = 322.6496907216495
Stdev insert size = 57.08645970234663
99.95 percentile insert size = 581.020000000015
Collecting signals on contig: 8
Collecting signals on contig: 11
('total', 0.3015010356903076)
Writing signals to file
extracted signals in:
-0.3036017417907715
calculated coverage in:
7.124830961227417
[M::main_ropebwt2] inserted 129948 symbols in 0.229 sec, 0.021 CPU sec
[M::main_ropebwt2] constructed FM-index in 0.229 sec, 0.021 CPU sec
[M::main_ropebwt2] symbol counts: ($, A, C, G, T, N) = (1274, 38888, 25449, 25449, 38888, 0)
[M::main_ropebwt2] rld: (tot, $, A, C, G, T, N) = (129948, 1274, 38888, 25449, 25449, 38888, 0)
[M::main] Version: r187
[M::main] CMD: /Users/islekbro/miniconda3/bin/ropebwt2 -dNCr /Users/islekbro/Desktop/SV/deneme3/manta_out_tiddit/clips.fa
[M::main] Real time: 0.234 sec; CPU: 0.029 sec
[M::fm6_unitig] choose prime 123457
[M::main] Version: r178
[M::main] CMD: /Users/islekbro/miniconda3/bin/fermi2 assemble -t 1 -l 81 -
[M::main] Real time: 0.309 sec; CPU: 0.078 sec
Clip read assembly in:
0.570451021194458
generated clusters in
0.0017549991607666016
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.8/bin/tiddit", line 11, in
load_entry_point('tiddit', 'console_scripts', 'tiddit')()
File "/Users/islekbro/TIDDIT/tiddit/main.py", line 167, in main
variants=tiddit_variant.main(bam_file_name,sv_clusters,args,library,min_mapq,samples,coverage_data,contig_number,max_ins_len)
File "tiddit/tiddit_variant.pyx", line 546, in tiddit.tiddit_variant.main
File "<array_function internals>", line 180, in percentile
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/lib/function_base.py", line 4166, in percentile
return _quantile_unchecked(
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/lib/function_base.py", line 4424, in _quantile_unchecked
r, k = _ureduce(a,
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/lib/function_base.py", line 3725, in _ureduce
r = func(a, **kwargs)
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/lib/function_base.py", line 4593, in _quantile_ureduce_func
result = _quantile(arr,
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/lib/function_base.py", line 4699, in _quantile
take(arr, indices=-1, axis=DATA_AXIS)
File "<array_function internals>", line 180, in take
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 190, in take
return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 57, in _wrapfunc
return bound(*args, **kwds)