search

jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
346 stars 81 forks source link

PacBio data with minimap2 and flye #773

Closed HannahBenisty closed 4 months ago

HannahBenisty commented 5 months ago

Hi, I have been trying to run the same pipeline for data coming from MinION and PacBIO in parallel. The analysis finishes with Nanopore data but with Pacbio there is an error. I here attache the syslog for Pacbio run. The parameters of the run are:

SqueezeMeta.pl -m sequential -s samplesfile.txt -map minimap2-pb -a flye -b 8

syslog.zip

Many thanks, Hannah

jtamames commented 5 months ago

Hello Hannah

There is a "SIGKILL: 9" in the syslog. This was produced by Flye when running your data. Given that Flye worked correctly when using minION, I would say this is a memory problem. How much RAM available does your computer have? Best, Javier

HannahBenisty commented 5 months ago

Hi Javier!

Thanks for your reply! I am working on the cluster and I have set up the virtual memory to 64gb and 12 cores.

Thanks, Hannah

jtamames commented 5 months ago

Hum... I am not that experienced in PacBio and Flye to know if that is sufficient. Could you monitor the memory usage somehow?

HannahBenisty commented 5 months ago

Sure, I will try! Thanks!

fpusan commented 4 months ago

Closing due to lack of activity, feel free to reopen