Segmentation fault when running ATHLATES

[Hang PHAN]

Hi,

I am new to ATHLATES and I have tried to follow the documentation on how to use it. I aligned the reads using MOSAIK aligner and then generated the bam files accordingly. 

However when I ran the typing program, I encountered segmentation error as below:

Running cmd:

./bin/typing -bam test_B.sort.bam -exlbam test_non-B.sort.bam -msa db/msa/B_nuc.txt -hd 2 -o test_B_Pred

--------------------------------------------------------

Obtain (un)paired-read names in test_non-B.sort.bam

#s&p names: 23989, 383585

create file: test_B_Pred.raw.fa

Finish creating output files

         Check BAM header of NHSBT_0001_B.sort.bam

[WARNING]: NHSBT_0001_B.sort.bam sort order: unsorted

Input BAM file should be sorted by queryname

8230 ref sequence(s) found; avg len = 905

1 platform(s) found: ILLUMINA

Merge PE for test_B.sort.bam

create file: test_B_Pred.unpair.fa

Finish creating output files

                Finish creating output files  

create file: test_B_Pred.pair.fa

Segmentation fault

----------------

I have tried to debug it but I could not figure out why there is this fault as it happens after creating the second output file  test_B_Pred.pair.fa,  which I found there should be no reason for such an error. 

Can you tell me what happened here and how to fix it?

Thanks,

Hang

[Xiao Yang]

Hi Hang,

This problem has been encountered by others previously.

We require that the input BAM files to ATHLATES contain ONLY reads that have been aligned.

The seg fault is most likely there exist some reads in the BAM file that have no alignment to

the reference ( you could check this by look at CIGAR string which is shown as * ).

hope this helps.

best,

Xiao 

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