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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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kegg.funcover is empty! #466

Closed aalkin2001 closed 2 years ago

aalkin2001 commented 2 years ago

I'm running metagenomic analysis with Sqeezemeta on data generated from nanopore minion sequence and using flye as the assembler. I got the error message below: How do I solve this issue?

Stopping in STEP12 -> 12.funcover.pl. /SqueezeMeta/metagenome_analysis/trial/trial_output/results/12.trial_output.cog.funcover and/or /home/akinola/mnt/data/tblab/working_dir/TFRI_Microbiome_analysis/SqueezeMeta/metagenome_analysis/trial/trial_output/results/12.trial_output.syslog.zip

jtamames commented 2 years ago

This is because you only have 4 contigs resulting from the assembly. Flye is a very strict assembler, but nevertheless you just have 244 Mb of sequence. If this is a metagenome, no way this can produce an usable assembly. Use sqm_longreads.pl to analyze the reads instead.