Error when running Dindel realignment stage

[ywy25]

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!

[ywy25]

Problem have been solved.
This error is caused by pair1 and pair2 fastq files are not in the same order.

[valei]

How did you solve the problem??

Dear ywy25,
con you explain exactly how you solved the problem you mentioned in the previous post?
I have the same problem, but I'm not understanding.
I am perfectly aware of the fact that the discussion goes back more than two years ago...anyway I hope in you have a great memory...
Many thanks