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I'm a bio major only recently doing major coding for research stuff. Our campus in order to support research has an on campus supercomputer for researcher use. I work remotely from this supercomputer and it uses a linux shell to access it and submit jobs. I'm writing a job submission script for the alignment of a lot of genomes using a program installed on the computer called Mauve. Now I've run a job on Mauve fine before and have altered the script from that job to fit this job. Only this time I keep getting this error

Storing raw sequence at
/scratch/addiseg/Elizabethkingia_clonalframe/rawseq16360.000
Sequence loaded successfully.
GCA_000689515.1_E27107v1_PRJEB5243_genomic.fna 4032057 base pairs.
Storing raw sequence at 
/scratch/addiseg/Elizabethkingia_clonalframe/rawseq16360.001
Sequence loaded successfully.
e.anophelisGCA_000496055.1_NUH11_genomic.fna 4091484 base pairs.
Caught signal 11
Cleaning up and exiting!
Temporary files deleted.

So I've got no idea how to troubleshoot this. I'm so sorry if this is super basic and wasting time but I don't know how to troubleshoot this at a remote site. All possible solutions I've seen so far require me to access the hardware or software neither of which I can control. My current submission script is this.

module load mauve 
progressiveMauve --output=8elizabethkingia-alignment.etc.xmfa --output-guide-tree=8.elizabethkingia-alignment.etc.tree --backbone-output=8.elizabethkingia-alignment.etc.backbone --island-gap-size=100 e.anophelisGCA_000331815.1_ASM33181v1_genomicR26.fna GCA_000689515.1_E27107v1_PRJEB5243_genomic.fna e.anophelisGCA_000496055.1_NUH11_genomic.fna GCA_001596175.1_ASM159617v1_genomicsrr3240400.fna e.meningoseptica502GCA_000447375.1_C874_spades_genomic.fna e.meningoGCA_000367325.1_ASM36732v1_genomicatcc13253.fna e.anophelisGCA_001050935.1_ASM105093v1_genomicPW2809.fna e.anophelisGCA_000495935.1_NUHP1_genomic.fna
shellter
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  • If the remote code isn't compiled with debug symbols, or you don't have permissions to run it in a debugger, you're going to need to get assistance from someone else. – Charles Duffy Mar 30 '16 at 21:41
  • ...you can also see about configuring the system to store a core dump, if ulimit settings &c. allow, and analyze that core dump, but without a debug build it's still not very usable/helpful. Short form: Talk to the people who wrote and maintain the software. – Charles Duffy Mar 30 '16 at 21:42
  • ...I also removed the bash tag: just because you're starting a program from a shell doesn't mean it's a shell-related question, unless that program is actually written as a shell script. – Charles Duffy Mar 30 '16 at 21:44
  • The program probably runs out of memory without noticing it. The only workaround you could try is: start the program for every sequence, but separately. You might need to create a script to accomplish this. (it looks like the program does a simple {input,process,output} loop for every sequence) – wildplasser Mar 30 '16 at 22:42

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