Segmentation fault when running Metabat

[Former user]

Hi, I've downloaded METABAT 10.2 (Linux 64), All seems fine and entering ./runMetaBat.sh yield this "./runMetaBat.sh <select metabat options> assembly.fa sample1.bam [ sample2.bam ...] etc ..

However when I call Metabat like indicated on your website: ./runMetaBat.sh <path to contigs.fa> <path to corresponding bam>, I obtain this error: ./runMetaBat.sh: line 118: 30797 Segmentation fault $MB $metabatopts --inFile $assembly --outFile $outname --abdFile ${depth} I've tried to give more memory, use relative or complete paths to no avail. Thanks for your help

[Rob Egan]

my first guess is that it still runs out of memory either on the stack or general allocation.

What is the RAM capacity of your machine and what are the sizes of the files that you are working with? bams? assembly? how many scaffolds are in the assembly?

I do not think that the static binary we distribute has debug symbols, so if it is not a memory limitation on your machine, we would need you to either compile the debug version and give us the full log after a run or let us run metabat your data here at the JGI.

[hudenise]

I have increased the memory as suggested but still the same issue. The assembly contains 32,226 contigs (size of fasta file: 76M) and the bam is 1G.

I tried to submit with 30, 60 and 90G of memory on LSF cluster.

My call was (from the metabat directory): bsub -q production-rh7 -M 60000 -o ../../ERP0XXXXX/megahit/ERRYYYYYY/metabat/log "./runMetaBat.sh ../../ERPXXXXX/megahit/ERRYYYYY/final.contigs.fa ../../ERPXXXXXX/megahit/ERRYYYYYY/ERRYYYYY.bam"

[Don Kang]

Why don't you send us your data?

For your convenience, I've requested a ftp service so that you can upload your data to our server. Please refer to information below. The easiest way is to use GUI ftp client like filezilla. Let me know if you have any issues. Thanks for your help.

[hudenise]

Hi Don,

Thanks for your quick answer, I've uploaded the assembly, the bam and the log from my attempts. let me know if you need anything else, cheers Hubert

[Don Kang]

Looks like the issue happened because your bam file was unsorted. It should be sorted first. Try this:

samtools sort scaffolds.bam scaffolds.sorted

and

runMetaBat.sh scaffolds.fasta scaffolds.sorted.bam

It produces 16 bins using metabat v2.11.1. Let us know if you still have any issue after making bam files sorted.

[hudenise]

Thanks Don,

indeed it worked. Version 0.32.5 yield 17 bins. Thanks for your help, Hubert

[Don Kang]

Great! We recommend you to try MetaBAT 2. It may work better! Good luck!