Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

KMC hangs #206

Open
jodyphelan opened this issue Dec 13, 2022 · 1 comment
Open

KMC hangs #206

jodyphelan opened this issue Dec 13, 2022 · 1 comment

Comments

@jodyphelan
Copy link

I am running kmc off a fastq file and mostly it runs ok. However, sometimes it hangs for no apparent reason. The command I am running is:

kmc -v -sm -m8 -t2 -sf2 -sp2 -sr2 -k25 @fc1f8619-bc09-460b-b29b-7e490eb0c188.list out .

The c1f8619-bc09-460b-b29b-7e490eb0c188.list file contains the following output:

./1b33b732-1720-4e18-8e1c-d9de4c78a87d.spacers.fq.txt

Usually it completes in about two seconds, but occasionally it will just indefinitely hang.
Here are the reads I am running it on: 1b33b732-1720-4e18-8e1c-d9de4c78a87d.spacers.fq.txt

This is the output:

********** Used parameters for Stage 1 : **********
No. of input files           : 1
Output file name             : 
No. of working directories   : 1
Input format                 : FASTQ
Output format                : KMC

k-mer length                 : 25
Max. k-mer length            : 256
Signature length             : 9
Both strands                 : true
RAM only mode                : false

******* Stage 1 configuration: *******

No. of bins                  : 512
Bin part size                : 65536
Input buffer size            : 12582912

No. of readers               : 2
No. of splitters             : 2

Max. mem. size               :  8000MB
Max. mem. per storer         :  3934MB
Max. mem. for single package :    15MB

Max. mem. for PMM (bin parts):  6052MB
Max. mem. for PMM (FASTQ)    :  1264MB
Max. mem. for PMM (reads)    :     2MB
Max. mem. for PMM (b. reader):   679MB

Stage 1: 100%
                                                                                                                                                                                      
********** Used parameters for Stage 2 : **********
Min. count threshold         : 2
Max. count threshold         : 1000000000
Max. counter value           : 255

******* Stage 2 configuration: *******
No. of threads               : 2

Max. mem. for 2nd stage      :    16MB

Stage 2: 100%
@jodyphelan
Copy link
Author

Just to follow up, if I leave out the -sm flag it seems to be ok (tested with 1000 iterations)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant