Dear Erica,

to check if it is a memory error, could you please paste the output of the following commands.

To retrieve the amount of memory in your machine:

free -h

To get the maximum resident set size used by a command:

/usr/bin/time --verbose <your_command>

Where <your_command> is your KisSplice command. After <your_command> finishes executing, time --verbose will output some log information that might help us debug. As a concrete example, we need the information that looks like this:

    Command being timed: "ls"
User time (seconds): 0.00
System time (seconds): 0.00
Percent of CPU this job got: 0%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
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): 2540
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 119
Voluntary context switches: 1
Involuntary context switches: 4
Swaps: 0
File system inputs: 0
File system outputs: 0
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0

Thanks for the report!

Kind regards.

May thanks for the response.

We're running this on a national computing cluster, with fairly substantial memory available. The most we've tried allocating thus far was 105GB and 36 cores. This ran but stopped without reporting an obvious error. However, I see this error buried in the output:

^MLooping through branching kmer n° 276197100 / 276236278     ^MLooping through branching kme**Problem with /nesi/nobackup/nesi00431/miniconda_envs/kisspl/libexec/kissplice/ks_debruijn4**r n° 276197400 / 276236278     ^MLooping through branching kmer n° 276197700 / 2
    76236278     ^MLooping through branching kmer n° 276198000 / 276236278    
    -------------------nodes construction time Wallclock  1370.73 s

Others runs have exited with this same error, but without proceeding into the analysis.
Here's the time report on that run:
    Command exited with non-zero status 247
    User time (seconds): 12789.24
    System time (seconds): 535.01
    Percent of CPU this job got: 100%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 3:41:58
    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): 49623228
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 0
    Minor (reclaiming a frame) page faults: 111321692
    Voluntary context switches: 1853865
    Involuntary context switches: 13397
    Swaps: 0
    File system inputs: 0
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
Exit status: 247

Any insights into the problem would be greatly appreciated.

Thanks again for the quick response. Happy to say we were able to run KisSplice to completion by installing on a different server. Seems likely something in the configuration of the previous server may have interfered with memory allocation at some stage, despite requesting sufficient memory in the script.

Thanks again.

Hello,

happy to hear it worked out for you!

Kind regards.