Question: Kissplice "Finding BCCs" and no output fa or tsv files
gravatar for audrahuffmeyer
16 days 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 • 105 views
ADD COMMENTlink modified 15 days ago by leandro.ishi.lima40 • written 16 days 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 16 days ago by Ram13k
gravatar for leandro.ishi.lima
15 days ago by
leandro.ishi.lima40 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 15 days ago by leandro.ishi.lima40

Thank you! This solved the problem!

Best, Audra

ADD REPLYlink written 13 days ago by audrahuffmeyer0
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