Hello sequencing gurus,
I am trying to setup a pipeline to analyze NGS data. I have been having trouble with 2 programs in particular (breakdancer_max and pindel). In regards to pindel, I have a correctly sorted and indexed bam file for input and the output looks like this (for every chromosome):
*** Calling SV using Split-Read Analysis: /home/usr/apps/pindel024s/src ***
>> Running Pindel on ALL: /home/usr/apps/pindel024s/src/pindel -f /srv/gs1/projects/lab/usr/data/hg19/ucsc.hg19.fasta -i /srv/gs1/projects/lab/usr/dir.2/JS2.sra.cfg -o /srv/gs1/projects/lab/usr/dir.2/JS2.sra -c ALL
Pindel version 0.2.4s, June 18 2012.
Looping over all chromosomes.
Processing chromosome: chrM
Chromosome Size: 16571
NumBoxes: 60020 BoxSize: 667
Looking at chromosome chrM bases 0 to 10000000.
getReads chrM 20016571
Insertsize in bamreads: 195
Number of reads in current window: 0, + 0 - 0
Number of reads where the close end could be mapped: 0, + 0 - 0
Percentage of reads which could be mapped: + 0.00% - 0.00%
No currentState.Reads for chrM found in /srv/gs1/projects/lab/usr/dir.2/JS2_L1_1_pf_aa.sorted.recal.bam
BAM file index 0 0
There are no reads for this bin.
And the configuration file looks like this:
/srv/gs1/projects/lab/usr/dir.2/JS2_L1_1_pf_aa.sorted.recal.bam 195 JS2
I can't figure out what's wrong. I originally used an older version and then reinstalled the latest version of pindel (0.2.4s) and I get the same problem, the "BAM file index 0 0" "no reads in this bin" for every bin for every chromosome.
Has anyone encountered a problem like this and been able to solve it? Any ideas would be really helpful.
Thanks.
I am trying to setup a pipeline to analyze NGS data. I have been having trouble with 2 programs in particular (breakdancer_max and pindel). In regards to pindel, I have a correctly sorted and indexed bam file for input and the output looks like this (for every chromosome):
*** Calling SV using Split-Read Analysis: /home/usr/apps/pindel024s/src ***
>> Running Pindel on ALL: /home/usr/apps/pindel024s/src/pindel -f /srv/gs1/projects/lab/usr/data/hg19/ucsc.hg19.fasta -i /srv/gs1/projects/lab/usr/dir.2/JS2.sra.cfg -o /srv/gs1/projects/lab/usr/dir.2/JS2.sra -c ALL
Pindel version 0.2.4s, June 18 2012.
Looping over all chromosomes.
Processing chromosome: chrM
Chromosome Size: 16571
NumBoxes: 60020 BoxSize: 667
Looking at chromosome chrM bases 0 to 10000000.
getReads chrM 20016571
Insertsize in bamreads: 195
Number of reads in current window: 0, + 0 - 0
Number of reads where the close end could be mapped: 0, + 0 - 0
Percentage of reads which could be mapped: + 0.00% - 0.00%
No currentState.Reads for chrM found in /srv/gs1/projects/lab/usr/dir.2/JS2_L1_1_pf_aa.sorted.recal.bam
BAM file index 0 0
There are no reads for this bin.
And the configuration file looks like this:
/srv/gs1/projects/lab/usr/dir.2/JS2_L1_1_pf_aa.sorted.recal.bam 195 JS2
I can't figure out what's wrong. I originally used an older version and then reinstalled the latest version of pindel (0.2.4s) and I get the same problem, the "BAM file index 0 0" "no reads in this bin" for every bin for every chromosome.
Has anyone encountered a problem like this and been able to solve it? Any ideas would be really helpful.
Thanks.
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