terminate called after throwing an instance of 'CThreadCancellationException'

[mkellom]

Not sure what this error means:

Stage 2: 56%terminate called after throwing an instance of 'CThreadCancellationException'
Command terminated by signal 6
Command being timed: "/usr/local/bin/kmc -t8 -fq -b -ci1 -cs65535 -k54 -m12 /illumina/05/24/63/52463.2.341579.AGTCAGGA-AGTCAGGA.fastq.gz splash-tmp-e792b903069d436fa2387adf47b28278/1281142 splash-tmp-e792b903069d436fa2387adf47b28278/kmc_tmp_1281142"
User time (seconds): 244.89
System time (seconds): 30.00
Percent of CPU this job got: 341%
Elapsed (wall clock) time (h:mm:ss or m:ss): 1:20.45
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 10658580
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 3082700
Voluntary context switches: 1884551
Involuntary context switches: 5516
Swaps: 0
File system inputs: 0
File system outputs: 60139152
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0

[marekkokot]

Hi, can you share your input data, or at least this file /illumina/05/24/63/52463.2.341579.AGTCAGGA-AGTCAGGA.fastq.gz ?

[mkellom]

Hi,

After talking with Julia Salzman a few days ago, we decided to try out SPLASH on metagenome data to see what it could find and get an idea of what the output looks like for this kind of run. My input file is a list of 500 metagenomes. File 52463.2.341579.AGTCAGGA-AGTCAGGA.fastq.gz can be downloaded here in the Raw Data folder: https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Aciome_2_FD

Thank you!