Varid crashes when read is aligned outside the chromosome

[Francisco Roque]

Hi,

I am trying to use varid as an alternative for diBayes for SNP calling
in Solid data. My reference organism is yeast, and I am taking the bam
file that Corona Lite produces, converting it to sam beforehand. The
problem is that some of the reads are aligned in the edge of the
chromosomes, and varid crashed when it finds the reads are placed
incorrectly (this particular read is aligned in position 230171, and
is 50bp long). Here is the error message:


samtools view -h maToBam/
ugc_432_solid0105_20110211_FRAG_BC_ugc_432_F3_ugc_432_32.csfasta.ma.bam
| varid_exec -r ../../../../reference/yeast/scerevisiae_concat.fasta -
o test --threads 8 --drop-bad-reads
Using 8 threads
Dropping bad reads, instead of exiting on bad reads

- alignments: stdin
- ref-file: ../../../../reference/yeast/scerevisiae_concat.fasta

Detected:
I:230218 nt
II:813184 nt
III:316620 nt
IV:1531933 nt
V:576874 nt
VI:270161 nt
VII:1090940 nt
VIII:562643 nt
IX:439888 nt
X:745751 nt
XI:666816 nt
XII:1078177 nt
XIII:924431 nt
XIV:784333 nt
XV:1091291 nt
XVI:948066 nt
M:85779 nt
Splitting reads
Total reads: 5963809
Used reads: 5963809
Done: in: 57.778 secs
------------------------------
Processing fasta entry : I - 230218bp
Processing group number : 1
Loading reads ...
Read "777_1261_104" has run off the end of genome, index 230219 vs
genome length 230218!
<run_wrap.c:781> varid_exec exiting...
<run_wrap.c:784> varid_exec exited

Any suggestions on how to fix this?

Regards

[Francisco Roque]

Figured out it works if I use a concatenated fast file for the entire
genome, but now I get memory errors (the machine has 128GB of memory,
so this shouldn't happen)

varid_exec -r ../../../../reference/yeast/scerevisiae_noheaders.fasta -
o test --threads 8 -a test.sam
Using 8 threads

- alignments: test.sam
- ref-file: ../../../../reference/yeast/
scerevisiae_noheaders.fasta

Detected:
sc288:12157105 nt

Splitting reads
Total reads: 5963809

Used reads: 0
Done: in: 4.032 secs
------------------------------
Processing fasta entry : sc288 - 12157105bp

Processing group number : 1
Loading reads ...

Done in 0.000 secs
Aligning reads ...
There are 0 potential insert sites
Done in: 0.000 secs
Starting VARiD Algorithm
Building Transition Matrix...
Done in: 0.054 secs
Trying to allocate 243142100 bytes...
covmaps built in: 3.478 secs, Used reads in the covmaps: 0/0,
Skipped for 0 index:0
Computing emissions...
SNP penalty 1.000000e-03, log -6.907755e+00
./tools/va_utils.c: 463 , out of memory!