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.
It’s most likely a RAM issue. What region are you sequencing? How many uniques? Are you trying to use
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.
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.
Might want to be aware of this timeless blog post.
This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.