Hello,
I am trying to use bowtie on small synthetic data for short read mapping. My command is
./bowtie -p 8 -t -S hg19 -1 synthetic_sample1.fq -2 synthetic_sample2.fq > bowtie.sam. The alignment stats is really bad.Seeded quality full-index search: 00:03:12
# reads processed: 1000003
# reads with at least one reported alignment: 129 (0.01%)
# reads that failed to align: 999874 (99.99%)
Reported 129 paired-end alignments to 1 output stream(s)
Time searching: 00:03:17
Overall time: 00:03:17
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
My error log says the following almost with every read I think. So the error log is a long list of similar errors
Warning: Exhausted best-first chunk memory for read chrY_25607312_25607822_7:0:0_4:0:0_13d4/1 (patid 986138); skipping read
When I googled the warning, I saw some suggestions of using --chunkmbs while running bowtie. I am not really sure what that does. I coudn't understand it from the manual. Still I used it with this command as it was suggested in one of the forums ./bowtie -p 8 -t --chunkmbs 256 -S hg19 -1 synthetic_sample1.fq -2 synthetic_sample2.fq > bowtie.sam. Then my error log saysTime loading reference: 00:00:01
Time loading forward index: 00:00:01
Time loading mirror index: 00:00:02
Error: Could not allocate ChunkPool of 268435456 bytes
Warning: Exhausted best-first chunk memory for read Error: Could not allocate ChunkPool ...