Early termination in step (2/10)

[pmhgrt]

Dear @barryghall & @shea0,

We just tried to use some Candida auris assemblies using kSNP4.1. We have multiple contigs in each files. We tried to run the program but we got a early termination in step 2.

(base) pmh@pmh-Alienware-Aurora-R13:~/program/kSNP4.1/Test/CAUR$ /home/pmh/program/kSNP4.1/kSNP4.1_Linux_package/kSNP4.1_Linux_package/kSNP4.1pkg/kSNP4 -in Test01.in -outdir Run1 -k 11 | tee Run3Log
fasta_list: /home/pmh/program/kSNP4.1/Test/CAUR/Test01.in
Output directory: /home/pmh/program/kSNP4.1/Test/CAUR/Run1
Starting kSNP4.1
Thursday, December 07, 2023 PM06:28:05 HKT
Configuration for this run:
input fasta_list: /home/pmh/program/kSNP4.1/Test/CAUR/Test01.in
output / working directory: /home/pmh/program/kSNP4.1/Test/CAUR/Run1
k=11
annotate_list file:
Maximum number of open files: 10240
Automatically determining number of CPUs to use:
The operating system is Linux
Discovered 24
Number CPUs: 24
Python version to be used:
Python 3.9.17
SNPS_ALL_INPUT=
GENBANKFILEINPUT=
CORE=0
ML=0
NJ=0
VCF=0
DEBUG=0
[00:00:00] (1/10) Preprocessing
[00:00:00] (2/10) Running jellyfish to get kmer counts

We also tried to delete the multiple contigs into only one contig and it run completely.

May we know if kSNP4.1 could only handle one contig per fasta file?

Thanks a lot.

Best regards,
GRT

[Rita]

This is happening to me as well. I don't think it's due to only handling one contig per file as I was previously able to successfully run over 150 samples each with 16 contigs in the individual files. However, now I have about 172 samples (each with 16 contigs) and now it hangs and crashes on that step. Is there something I can add to the command I am using to account for more memory or CPU?

[Barry G. Hall]

You are probably running out of RAM.
Barry G. Hall
barryghall@gmail.com



On Feb 12, 2024, at 11:39 AM, Rita rimo2@users.sourceforge.net wrote:

This is happening to me as well. I don't think it's due to only handling one contig per file as I was previously able to successfully run over 150 samples each with 16 contigs in the individual files. However, now I have about 172 samples (each with 16 contigs) and now it hangs and crashes on that step. Is there something I can add to the command I am using to account for more memory or CPU?

Early termination in step (2/10) https://sourceforge.net/p/ksnp/discussion/general/thread/faa46b0eac/?limit=25#0bbb
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[Rita]

It was the RAM on those samples and I was able to fix it and have it run. However, those were on assembled genomes and now I am trying to run with raw (quality checked and trimmed) paired-end combined Illumina fasta files and it hangs on the second step. I have attached the log file describing the error.

[Rita]

[hansen wang]

the error you encounter is the same as me. Do you get some response for this, how do you resolve this?