varid error

[vidhya]

Hi all

I have sam file from Shrimp alignment of ABI solid paired reads to the
reference genome.
The reference sequence consists of four regions from four different
chromosomes. Here is the header from the sam file

@HD VN:1.0 SO:unsorted
@SQ SN:BTA01_UMD-3.0_1582828-2049400 LN:466393
@SQ SN:BTA03_UMD-3.0_117657344-119144385 LN:1487042
@SQ SN:BTA06_UMD-3.0_71752844-72277600 LN:524757
@SQ SN:BTA17_UMD3.0_55853187-57599455 LN:1746269

The sam file was generated using the following command:
gmapper-cs -E -I 0,250 -V -n 2 -v 55% -Z -h 60% -i -10 -1
solid0175_20101005_PE_GUI21_F3.csfasta -2
solid0175_20101005_PE_GUI21_F5-P2.csfasta -p opp-in
BTA_p703_target_enrich.fa

Now when I ran varid with the following command, I get the following
error.
varid_exec -r BTA_p703_target_enrich.fa -a mapped1_2.sam -o
mapped1_2_var.pb --threads 4

I get the following error and the output file is empty. Not sure where
I am going wrong.


Using 4 threads

- alignments: mapped1_2.sam
- ref-file: BTA_p703_target_enrich.fa

Detected:
BTA01_UMD-3.0_1582828-2049400:466393 nt
BTA03_UMD-3.0_117657344-119144385:1487042 nt
BTA06_UMD-3.0_71752844-72277600:524757 nt
BTA17_UMD3.0_55853187-57599455:1746269 nt
Splitting reads
Total reads: 62306038
Used reads: 62306038
Done: in: 411.027 secs
------------------------------
Processing fasta entry : BTA01_UMD-3.0_1582828-2049400 - 466393bp
Processing group number : 1
Loading reads ...
Done in 54.112 secs
Aligning reads ...
There are 6708 potential insert sites
Done in: 126.710 secs
Starting VARiD Algorithm
Building Transition Matrix...
Done in: 0.041 secs
Trying to allocate 633955340 bytes...
covmaps built in: 108.208 secs, Used reads in the covmaps:
5503780/5503780, Skipped for 0 index:0
Computing emissions...
SNP penalty 1.000000e-03, log -6.907755e+00
Done in: 456.871 secs,
fwd algo done in: 295.053 secs
bwd algo done in: 216.511 secs
DONE VARiD Algorithm & prediction in: 1120.508 secs
Starting primary prediction... Done in: 308.574 secs
<nuc2col.c:143> assertion: (outcol_tmp.data[i] != (VA_UINT8)-1)
failed, Last errno=34
<run_wrap.c:781> varid_exec exiting...
<run_wrap.c:784> varid_exec exited


Thank you very much for your answers.

[Misko Dzamba]

Hi Vidhya,
I believe this problem is fixed in the new version of VARiD. There has
been quite a few bug fixes, and will be released soon. I can get you a
copy in a few hours to test out, to see if it still has the same
error.

Misko

[vidhya]

Hi Misko

Thats great. Thank you very much.

Vidhya