Open jodyphelan opened 1 year ago
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%
Just to follow up, if I leave out the -sm flag it seems to be ok (tested with 1000 iterations)
-sm
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:
The c1f8619-bc09-460b-b29b-7e490eb0c188.list file contains the following output:
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: