Hi kai,
I met a problem when I run pindel.
this is the command line:
pindel -f ../ref/hs_ref_GRCh37.p2.all.fa -i config.txt -c all -o pindeloutput -T 8
this is the configure file:
A1.sort.bam 300 A1
A2.sort.bam 300 A2
A3.sort.bam 300 A3
the bam files were generated by BWA, I also try the unsorted bam file, not work too.
this is the prompt:
Pindel version 0.2.4o, March 9 2012.
Processing chromosome: gi|224589800|ref|NC_000001.10|
Skipping chromosome: gi|224589800|ref|NC_000001.10|
Processing chromosome: gi|224589811|ref|NC_000002.11|
Skipping chromosome: gi|224589811|ref|NC_000002.11|
Processing chromosome: gi|224589815|ref|NC_000003.11|
Skipping chromosome: gi|224589815|ref|NC_000003.11|
.............
Processing chromosome: gi|224514683|ref|NT_167243.1|
Skipping chromosome: gi|224514683|ref|NT_167243.1|
Processing chromosome: gi|251831106|ref|NC_012920.1|
Skipping chromosome: gi|251831106|ref|NC_012920.1|
Loading genome sequences and reads: 0 seconds.
Mining, Sorting and output results: 0 seconds.
could you help me to solve this problem?
Regards
Yongbiao
I met a problem when I run pindel.
this is the command line:
pindel -f ../ref/hs_ref_GRCh37.p2.all.fa -i config.txt -c all -o pindeloutput -T 8
this is the configure file:
A1.sort.bam 300 A1
A2.sort.bam 300 A2
A3.sort.bam 300 A3
the bam files were generated by BWA, I also try the unsorted bam file, not work too.
this is the prompt:
Pindel version 0.2.4o, March 9 2012.
Processing chromosome: gi|224589800|ref|NC_000001.10|
Skipping chromosome: gi|224589800|ref|NC_000001.10|
Processing chromosome: gi|224589811|ref|NC_000002.11|
Skipping chromosome: gi|224589811|ref|NC_000002.11|
Processing chromosome: gi|224589815|ref|NC_000003.11|
Skipping chromosome: gi|224589815|ref|NC_000003.11|
.............
Processing chromosome: gi|224514683|ref|NT_167243.1|
Skipping chromosome: gi|224514683|ref|NT_167243.1|
Processing chromosome: gi|251831106|ref|NC_012920.1|
Skipping chromosome: gi|251831106|ref|NC_012920.1|
Loading genome sequences and reads: 0 seconds.
Mining, Sorting and output results: 0 seconds.
could you help me to solve this problem?
Regards
Yongbiao
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