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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
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Error Encountered in SqueezeMeta with PacBio data #860

Open Meeenakshipari opened 3 days ago

Meeenakshipari commented 3 days ago

I am using SqueezeMeta to analyze PacBio data. The first step in SqueezeMeta is to run Canu because it is suited for PacBio data. However, I encountered an error during this step. Here are the details: I am using SqueezeMeta with PacBio data from SRR IDs SRR5219184 and SRR5219191 (human gut metagenome). Canu was chosen for assembly due to its compatibility with PacBio data, but the assembly process failed during the Canu step, displaying an error message related to low coverage. I have referred to Canu issue #1795, which suggested setting corOutCoverage=10000, corMhapSensitivity=high, and corMinCoverage=0. Despite these changes, the low coverage issue persists. Could you provide additional suggestions or parameter adjustments to resolve this low coverage issue and ensure successful assembly of the metagenomes?

Any help would be greatly appreciated.

I have attached the syslog file and error also,

canu_error

syslog.zip

fpusan commented 1 day ago

This seems like a canu issue and we might not be the best people to ask. By reading the message, adding stopOnLowCoverage=8 should probably make it work. Alternatively, flye, which is also distributed together with SqueezeMeta, should be able to take PacBio reads too.