Pindel Config File Error

Question

[pwiner]

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

Answer 1

[eherman]

I know this question is old, but I ran into the same issue and could not find any help online.

If you are trying to run Pindel with a config file and see the error

Something wrong with the read name: [first line of config file]

This happens when the config file is specified with -p when it should be specified with -i.

The following command should work:

pindel -f /auto/lai-00/rkl1/muskens/glioma/refgenome/hs38DH.fa -i 120207_config.txt -c ALL -o 120207