Question: Kissplice "Finding BCCs" and no output fa or tsv files
gravatar for audrahuffmeyer
4 months ago by
audrahuffmeyer0 wrote:

I am running the kissplice program on 8 fastq files. Everything runs until "Finding the BCCs" (see summary log below). Then the program stops and there is no output. I do not get any tsv files. This has happened twice now, do I need to change the --timeout parameters?

Thanks in advance!

[09:55:58 03/03/2018] --> Building de Bruijn graph...
Graph will be written in results/graph_480_001_480_002_494_001_494_002_499_001_499_002_500_001_500_002_CW1_001_CW1_002_CW4_001_CW4_002_CW1F2_001_CW1F2_002_CW2F2_001_CW2F2_002_k41.[edges/nodes]
[10:46:40 04/03/2018] --> Done!
Elapsed time: 89442.2153039 seconds

[10:46:40 04/03/2018] --> Removing sequencing errors...
[00:56:52 05/03/2018] --> Done!
Elapsed time: 51011.570462 seconds

[00:56:52 05/03/2018] --> Finding the BCCs...
kissplice twas • 223 views
ADD COMMENTlink modified 4 months ago by leandro.ishi.lima70 • written 4 months ago by audrahuffmeyer0

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time. Formatting bar

ADD REPLYlink written 4 months ago by Ram15k
gravatar for leandro.ishi.lima
4 months ago by
leandro.ishi.lima70 wrote:

Dear audrahuffmeyer,

There is a common problem in this step if your graph is too large and your stack size is not sufficiently large for the several calls of a recursive algorithm. To solve this problem, try to run (in Unix systems):

ulimit -s unlimited

before running KisSplice.

If you are using a Mac OS, try:

ulimit -H -s

to find the highest value possible for the stack size and then:

 ulimit -s <highest_value>

to set the new value of the stack size.

Could you please tell me if this worked for you?


Kind regards.

ADD COMMENTlink written 4 months ago by leandro.ishi.lima70

Thank you! This solved the problem!

Best, Audra

ADD REPLYlink written 4 months ago by audrahuffmeyer0
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