Error with make.contigs

1

Hi,

I am currently running mothur in batch mode (Linux version, mothur v.1.48.0), however I seem to be running into trouble at the very first step. Although the make.contigs step begins sucessfully, it seems to crash abruptly mid-run returning a termination message with an exit status 137 (I am running mothur in HPC). I believe that this refers to a memory problem. To resolve this, I tried to increase my total memory to 70 gb, 75 gb, 80 gb and even 150 gb while reducing the number of processors. I still end up with an exit status 137 no matter how high I increase the total memory.

This is the output from my error file.

/var/spool/torque/mom_priv/jobs/51312465.tier2-p-moab-2.tier2.hpc.kuleuven.be.SC: line 20: 8077 Killed

I have a total dataset size of ~48gb in the gz format. I would be sincerely grateful if you could help me resolve this issue!

Many many thanks!

Aditi

2

Hi Aditi - those files aren’t excessively large. I wonder if there are any other error messages. Could you post the entire mothur logfile that is generated?

Pat

3

Hi Pat,

It seems that the problem was not with mothur, but with the fastq.gz files that were corrupted during the download. All seems to be working now!

My apologies!

Aditi

4

That’s fantastic! Glad to hear you got it working

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