Entering edit mode
5.0 years ago
pwiner
▴
10
Hello, I am trying to run pindel using the required BAM config file and I get the following error :
pindel -f /auto/lai-00/rkl1/muskens/glioma/refgenome/hs38DH.fa -p 120207_config.txt -c ALL -o 120207
Initializing parameters...
Pindel version 0.2.5b9, 20160729.
Loading reference genome ...
Loading reference genome done.
Initializing parameters done.
SearchRegion::SearchRegion
Processing region: chr1 1 248956422
Chromosome Size: 248956422
NumBoxes: 60002 BoxSize: 8305
Looking at chromosome chr1 bases 1 to 5000001 of the bed region: chromosome chr1:1-248956422
Scanning and processing reads anchored in chr1
Something wrong with the read name: 120207.recaled.bam 348 120207.recaled
malformed record detected in 120207_config.txt
Any idea what is wrong with my config file?
Regards,
Peleg