I am using lumpyexpress on my Whole genome sequencing data. My command is: /data1/sjiang4/soft/lumpy-sv/bin/lumpyexpress -B /data1_2/ywang59/SCZ_Reheader_Bamfile/VCU00C02390.bam -o /data1_3/sjiang4/sv/lumpy/VCU00C02390.lumpy.vcf
It returned me this error info:
Sourcing executables from /data1/sjiang4/soft/lumpy-sv/bin/lumpyexpress.config ...
Checking for required python modules (/home/sjiang4/anaconda2/bin/python)...
/data1/sjiang4/soft/lumpy-sv/bin/lumpyexpress: line 389: --acceptDupMarks: command not found
Warning: only 0 elements in distribution (min: 1000)
Traceback (most recent call last):
File "/data1/sjiang4/soft/lumpy-sv//scripts/bamkit/bamgroupreads.py", line 171, in
sys.exit(main())
File "/data1/sjiang4/soft/lumpy-sv//scripts/bamkit/bamgroupreads.py", line 167, in main
bamgroupreads(args.input, args.readgroup, args.reset_dups, args.fix_flags, args.S, args.b, args.u)
File "/data1/sjiang4/soft/lumpy-sv//scripts/bamkit/bamgroupreads.py", line 93, in bamgroupreads
out_bam.write(al)
File "pysam/libcalignmentfile.pyx", line 1701, in pysam.libcalignmentfile.AlignmentFile.write
File "pysam/libcalignmentfile.pyx", line 1735, in pysam.libcalignmentfile.AlignmentFile.write
IOError: sam_write1 failed with error code -1
I checked my lumpyexpress.config file, it's like this:
LUMPY_HOME=/data1/sjiang4/soft/lumpy-sv/
Should I install SAMBLASTER and set it and change '//' to be '/' for the python executable file paths in the .config file? Or is there any other thing I need to set?
Hi,
I am using lumpyexpress on my Whole genome sequencing data. My command is: /data1/sjiang4/soft/lumpy-sv/bin/lumpyexpress -B /data1_2/ywang59/SCZ_Reheader_Bamfile/VCU00C02390.bam -o /data1_3/sjiang4/sv/lumpy/VCU00C02390.lumpy.vcf
It returned me this error info: Sourcing executables from /data1/sjiang4/soft/lumpy-sv/bin/lumpyexpress.config ...
Checking for required python modules (/home/sjiang4/anaconda2/bin/python)... /data1/sjiang4/soft/lumpy-sv/bin/lumpyexpress: line 389: --acceptDupMarks: command not found Warning: only 0 elements in distribution (min: 1000) Traceback (most recent call last): File "/data1/sjiang4/soft/lumpy-sv//scripts/bamkit/bamgroupreads.py", line 171, in
sys.exit(main())
File "/data1/sjiang4/soft/lumpy-sv//scripts/bamkit/bamgroupreads.py", line 167, in main
bamgroupreads(args.input, args.readgroup, args.reset_dups, args.fix_flags, args.S, args.b, args.u)
File "/data1/sjiang4/soft/lumpy-sv//scripts/bamkit/bamgroupreads.py", line 93, in bamgroupreads
out_bam.write(al)
File "pysam/libcalignmentfile.pyx", line 1701, in pysam.libcalignmentfile.AlignmentFile.write
File "pysam/libcalignmentfile.pyx", line 1735, in pysam.libcalignmentfile.AlignmentFile.write
IOError: sam_write1 failed with error code -1
I checked my lumpyexpress.config file, it's like this: LUMPY_HOME=/data1/sjiang4/soft/lumpy-sv/
LUMPY=/data1/sjiang4/soft/lumpy-sv//bin/lumpy HEXDUMP=/bin/hexdump SAMBLASTER= SAMBAMBA=/data1/sjiang4/soft/bin/sambamba SAMTOOLS=/usr/local/bin/samtools PYTHON=/home/sjiang4/anaconda2/bin/python
PAIREND_DISTRO=/data1/sjiang4/soft/lumpy-sv//scripts/pairend_distro.py BAMGROUPREADS=/data1/sjiang4/soft/lumpy-sv//scripts/bamkit/bamgroupreads.py BAMFILTERRG=/data1/sjiang4/soft/lumpy-sv//scripts/bamkit/bamfilterrg.py BAMLIBS=/data1/sjiang4/soft/lumpy-sv//scripts/bamkit/bamlibs.py
Should I install SAMBLASTER and set it and change '//' to be '/' for the python executable file paths in the .config file? Or is there any other thing I need to set?
Thanks,
Shan