Question: Kissplice "Finding BCCs" and no output fa or tsv files
0
gravatar for audrahuffmeyer
11 weeks 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 • 171 views
ADD COMMENTlink modified 11 weeks ago by leandro.ishi.lima70 • written 11 weeks 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 11 weeks ago by Ram15k
0
gravatar for leandro.ishi.lima
11 weeks 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?

Thanks!

Kind regards.

ADD COMMENTlink written 11 weeks ago by leandro.ishi.lima70

Thank you! This solved the problem!

Best, Audra

ADD REPLYlink written 10 weeks ago by audrahuffmeyer0
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