Error with make.contigs


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/ 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!


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?


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!


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