Bowtie Problem

[BioTalk]

Hello All,

I am trying to align some of the sequences by using Bowtie but I am getting an error which I am not able to figure out.


hetal@hetal-laptop:/Desktop/bowtie-0.12.3$ ./bowtie -p 2 -k 40 -S -v 0 -a -t indexes/TAIR9INDEX -f ~/Desktop/Test1.fasta ~/Desktop/Test1.map
Time loading forward index: 00:00:00
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted

Thank you,

[damiankao]

it looks like you are running out of memory.

[BioTalk]

Do you know how could I can solve this problem?

[brentp]

lowering -k value should reduce the memory requirements. usually a value < 10 is more than sufficient.

[BioTalk]

Thank you for your help. Looks like it is working for -k value < 10. But I have a question regarding this parameter. Does it affects the result in anyway?

The manual says that -k value instructs Bowtie to report up to the given number of valid alignments.

Thank you,

[brentp]

well, if a read hits to more than 10 places, it is probably simple sequence (or very short read?) but with a mismatch of 0 as you have specified, i doubt you're losing any real alignments because of -k. you could run with -m 10 -- you may get a different result, but bowtie will report how many alignments it discarded because of that parameter which i think should give you an idea of the amount that were discarded when you ran with -k 10.

[BioTalk]

When I am trying to run some file in Bowtie, I get the result something like this:

bowtie$ bowtie -p 4 --solexa-quals -S -k 40 -v 0 indexes/tair9 ~/Desktop/A_080822.fq ~/Desktop/80822.sam
# reads processed: 4791894
# reads with at least one reported alignment: 3795532 (79.21%)
# reads that failed to align: 996362 (20.79%)
Reported 15026063 alignments to 1 output stream(s)

But for some other seq files, -k 40 peramerter is not working and throwing memory allocation error. But when I gave -k 9 it results something like this:

./bowtie -p 2 -k 9 -S -v 0 -a -t indexes/TAIR9INDEX -f /R.fasta /media/BlackArmor\ Drive/R.map
Time loading forward index: 00:00:00
Time for 0-mismatch search: 00:00:50
Time searching: 00:00:50
Overall time: 00:00:50

And when I look at the .map file for both this sample, the map file for the second one "R.map" looks kind of wearied.

Please let me know if anyone has got the same problem or knows the solution to this problem.

Thank you,