mothur

Zsh crash on Linux

Hello friends
I must need your help.
I am running mothur 1.41 in biolinux machine. I am analysing 16S rRNA illumina sequencing data. All my data is in an external hard-drive connected to the machine via usb port. Mothur is running directly in the data folder, so in the external hard-drive (4 Tb space). I decided to run all in the external drive due to a previous killed9 error, guessing a rather disk space issue than a software issue. Analyseswent smooth until analysing sequences at OTU level.
Dist.seqs takes its time, but finally complete .
However, while running cluster.split … it crashed with the message “zsh killed”.

Do you have any idea? can not be a disk space issue, there are still 2Tb free space. So I am wondeirng if it’s just a problem due to running mothur in an external drive or … buffering problem. In fact, I have no clues … any idea from the audience?

Thank you very much for any help of suggestion.

Marc

It’s most likely a RAM issue. What region are you sequencing? How many uniques? Are you trying to use cluster.split?

Also, FWIW, I suspect storing your data on a USB drive will make analysis painfully slow since USB transfer is slow and every time you read/write to disk, it will use the USB protocol to transfer the data.

Pat

Hey Pat

Thanks for your replay. We are sequencing V3V4 region (341f-806br). We have actually 540136 unique seqs of a total of 1084399 seqs according to summary script on 0mm16Slinux.trim.contigs.good.unique.fasta file.
Yes, I have been running cluster.split and it was while running it that crash.
Yes, I am totally agree with USB read/write issue … but by now it’s my best option. I am using a biolinux machine with 16Gb of RAM.
Again thanks for your constructive comments and time.

Yours

Marc

Might want to be aware of this timeless blog post.

Pat

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