Some SV callers failed in SVE call

[TendoLiu]

Of all the SV callers wrapped in SVE, some work well and some do not.
Error1:
loaded param_map from: breakdancer.json
using wrapper: breakdancer
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perl /tools/SVE/src/breakdancer-1.4.5/perl/bam2cfg.pl -q 30 -n 10000 /bgfs/soesterreich/pa n_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/SecondPanel/0_Illumina_UM I_Error_Corrected_bam/Sample1.collapsed.bam > /bgfs/soesterreich/pan_data/soesterreich/Ten do/Projects/Project2_cfDNA_fusion_capture/SecondPanel/1_SVcalling/SVE/Samples/Sample1.coll apsed_S4/bd_confg.txt
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/tools/SVE/src/breakdancer-1.4.5/build/bin/breakdancer-max /bgfs/soesterreich/pan_data/soe sterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/SecondPanel/1_SVcalling/SVE/Samples /Sample1.collapsed_S4/bd_confg.txt > /bgfs/soesterreich/pan_data/soesterreich/Tendo/Projec ts/Project2_cfDNA_fusion_capture/SecondPanel/1_SVcalling/SVE/Samples/Sample1.collapsed_S4. calls
call error:
message:
code: 1
output:
[Wed Oct 23 13:11:29 2019 /tools/SVE/src/breakdancer-1.4.5/perl/bam2cfg.pl] Processing bam : /bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/Se condPanel/0_Illumina_UMI_Error_Corrected_bam/Sample1.collapsed.bam
Use of uninitialized value $lib in hash element at /tools/SVE/src/breakdancer-1.4.5/perl/b am2cfg.pl line 79, <$bam> line 27.
[Wed Oct 23 13:13:03 2019 /tools/SVE/src/breakdancer-1.4.5/perl/bam2cfg.pl] Closing BAM fi le
[Wed Oct 23 13:13:03 2019 /tools/SVE/src/breakdancer-1.4.5/perl/bam2cfg.pl] Send TERM sign al for 27219
[Wed Oct 23 13:13:05 2019 /tools/SVE/src/breakdancer-1.4.5/perl/bam2cfg.pl] samtools pid p rocess 27219 is still there...
[Wed Oct 23 13:13:05 2019 /tools/SVE/src/breakdancer-1.4.5/perl/bam2cfg.pl] invoking kill -9 on 27219 ...
[Wed Oct 23 13:13:05 2019 /tools/SVE/src/breakdancer-1.4.5/perl/bam2cfg.pl] Closing samtoo ls process : 27219
Use of uninitialized value $lib in hash element at /tools/SVE/src/breakdancer-1.4.5/perl/b am2cfg.pl line 195.

{'output': '', 'message': '', 'code': 1}
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Error2:
loaded param_map from: hydra.json
using wrapper: hydra
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making the hydra configuration
/usr/local/bin/python /tools/SVE/src/hydra/scripts/make_hydra_config.py -i /bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/SecondPanel/1_SVcalling/SVE/Samples/Sample1.collapsed_S17/bam.stub -s 100000 -n 16 > /bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/SecondPanel/1_SVcalling/SVE/Samples/Sample1.collapsed_S17/bam.stub.config
extracting discordants for sample0
/usr/local/bin/python /tools/SVE/src/hydra/scripts/extract_discordants.py -c /bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/SecondPanel/1_SVcalling/SVE/Samples/Sample1.collapsed_S17/bam.stub.config -d sample0
call error: Traceback (most recent call last):
File "/tools/SVE/src/hydra/scripts/extract_discordants.py", line 212, in
main()
File "/tools/SVE/src/hydra/scripts/extract_discordants.py", line 204, in main
discordant_bam_query_sort = query_sort_discordant(discordant_bam, opts.mem)
File "/tools/SVE/src/hydra/scripts/extract_discordants.py", line 128, in query_sort_discordant
subprocess.call(shlex.split(sortCmd))
File "/usr/local/lib/python2.7/subprocess.py", line 168, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/local/lib/python2.7/subprocess.py", line 390, in init
errread, errwrite)
File "/usr/local/lib/python2.7/subprocess.py", line 1025, in _execute_child
raise child_exception
OSError: [Errno 13] Permission denied

message:
code: 1
output:

vcf file /bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/SecondPanel/1_SVcalling/SVE/Samples/Sample1.collapsed_S17.vcf exists=False
computing hydra breakpoints
grep -v "#" /bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/SecondPanel/1_SVcalling/SVE/Samples/Sample1.collapsed_S17/all-sv.calls.freq | /usr/local/bin/python /tools/SVE/src/hydra/scripts/hydraToBreakpoint.py -i stdin > /bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/SecondPanel/1_SVcalling/SVE/Samples/Sample1.collapsed_S17/all-sv.calls.bkpts
all hydra stages completed
{'output': 'Traceback (most recent call last):\n File "/tools/SVE/src/hydra/scripts/extract_discordants.py", line 212, in \n main()\n File "/tools/SVE/src/hydra/scripts/extract_discordants.py", line 204, in main\n discordant_bam_query_sort = query_sort_discordant(discordant_bam, opts.mem)\n File "/tools/SVE/src/hydra/scripts/extract_discordants.py", line 128, in query_sort_discordant\n subprocess.call(shlex.split(sortCmd))\n File "/usr/local/lib/python2.7/subprocess.py", line 168, in call\n return Popen(*popenargs, **kwargs).wait()\n File "/usr/local/lib/python2.7/subprocess.py", line 390, in init\n errread, errwrite)\n File "/usr/local/lib/python2.7/subprocess.py", line 1025, in _execute_child\n raise child_exception\nOSError: [Errno 13] Permission denied\n', 'message': '', 'code': 1}
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