megahit error exit code 6

Question

[v.berriosfarias]

Hello , I wanted to post this on the megahit issues GitHub page but I can't access to GitHub by now. The point is that I'm getting the following error message when I run this code:

megahit -1 fwd_reads.fastq.gz -2 rev_reads.fastq.gz --min-contig-len 500 -m 0.8 -o ${dir}/co_asembly_cl4_try3 -t 32 --presets meta-large

the above code is a co assembly of multiple setas of paired end reads.

Command: megahit_core assemble -s co_asembly_cl4_try3/tmp/k27/27 -o co_asembly_cl4_try3/intermediate_contigs/k27 -t 32 --min_standalone 500 --prune_level 2 --merge_len 20 --merge_similar 0.95 --cleaning_rounds 5 --disconnect_ratio 0.1 --low_local_ratio 0.2 --cleaning_rounds 5 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble; Exit code -6

what is this exit code message?

[Mensur Dlakic]

I am fairly certain that it can't be more than a handful of people in the world who can answer that question without looking it up, and those would be maybe program developers. It simply isn't something that many people commit to memory. The rest of us have to look it up, so you might do it as well by Googling megahit Exit code -6.

Answer 1

[Mensur Dlakic]

Even though I try not to encourage laziness, the curiosity got a better of me and I googled the error:

• https://github.com/voutcn/megahit/issues/270
• https://github.com/voutcn/megahit/issues/237

But really, what I said above stands. These are kinds of program errors where very few people in the world can help you without investing some effort. You might as well do the same before asking a question.