Hi all,
I'm running Dindel for calling small indels from whole-exome sequencing data.
I have finished pervious samples successfully. However, when I try to run another 13 samples, I got an error message at the stage 3:
matepos inconsistency!
14647035 14646905
So, there is nothing in the .glf.txt file and .vcf file.
This error happens on all the BAM files at the first realignment window.
I have got the .variants.txt file and .library file successfully.
Here is the command I used in stage 3:
./dindel-1.01-linux-64bit --analysis indels --doDiploid --bamFile chr22_17737.fa_sort.bam --ref ~/hg18/chr22.fa --varFile chr22_17737.fa.1.txt --libFile chr22_17737.fa.libraries.txt --outputFile chr22_17737.fa > chr22_17737.fa.out 2> chr22_17737.fa.err
In the screen output for stage 3, it stopped at:
****
tid: chr22 pos: 14646919 leftPos: 14646860 rightPos: 14646979
Fetching reads....
Maybe there is a problem when fetching reads from the BAM files caused by "matepos inconsistency"?
Is there anyone can help me?
Many thanks!
I'm running Dindel for calling small indels from whole-exome sequencing data.
I have finished pervious samples successfully. However, when I try to run another 13 samples, I got an error message at the stage 3:
matepos inconsistency!
14647035 14646905
So, there is nothing in the .glf.txt file and .vcf file.
This error happens on all the BAM files at the first realignment window.
I have got the .variants.txt file and .library file successfully.
Here is the command I used in stage 3:
./dindel-1.01-linux-64bit --analysis indels --doDiploid --bamFile chr22_17737.fa_sort.bam --ref ~/hg18/chr22.fa --varFile chr22_17737.fa.1.txt --libFile chr22_17737.fa.libraries.txt --outputFile chr22_17737.fa > chr22_17737.fa.out 2> chr22_17737.fa.err
In the screen output for stage 3, it stopped at:
****
tid: chr22 pos: 14646919 leftPos: 14646860 rightPos: 14646979
Fetching reads....
Maybe there is a problem when fetching reads from the BAM files caused by "matepos inconsistency"?
Is there anyone can help me?
Many thanks!
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