Metabat2 Segmentation fault

I got a problem when I run metabat2 from my lab server. I've installed metabat2 with conda. So, it does not generate bins because of a problem of segmentation fault

Here is the log file output:

$ head -n 50 generate_bin_china_v4.log

nohup: ignoring input
Output depth matrix to bins_paired/depth_ERR1018185_M2-Pk008A.SZAXPI003409-8.txt
Output matrix to bins_paired/depth_ERR1018185_M2-Pk008A.SZAXPI003409-8.txt
Opening 1 bams
Consolidating headers
Processing bam files
Thread 0 finished: ERR1018185_M2-Pk008A.SZAXPI003409-8_sorted_index.bam with 60749206 reads and 50677626 readsWellMapped
Creating depth matrix file: bins_paired/depth_ERR1018185_M2-Pk008A.SZAXPI003409-8.txt
Closing most bam files
Closing last bam file
Finished
MetaBAT 2 (v2.12.1) using minContig 2500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, and maxEdges 200.
generate_bins.sh: line 12: 1808964 Segmentation fault      metabat2 -i "$CONTIG" -a "$DEPTH" -o "$BIN_OUT/bin"

segmentationfault metabat2

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written 7 months ago by Edson •

seg faults can be due to memory limits/errors. Have you monitored the memory usage on the server to see if the job is running out of memory?

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written 7 months ago by GenoMax

1 answer

Thanks for the quickly reply. I updated metabat2 conda version and added -t flag. It solved it.

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written 7 months ago by Edson •