Segmentation fault

[vpymerel]

Hello,

I am using hifiasm to assemble HiFI reads (Genome size ~ 600 Mb, fastq.gz ~ 6Go),

Similarly to https://github.com/chhylp123/hifiasm/issues/69 I got a segmentation fault when "Writing reads to disk... ", but using v > 0.14 does not work for me (I am using 0.16.1),

Here is the command used: hifiasm -t 20 -o results/X/hifiasm/hifiasm data/X.fastq.gz

I am running it with 20 cores and 100Gb of RAM.

The log is attached. hifiasm.txt

Can you help me please ?

Thank you,

V

[chhylp123]

Can you make sure that there is enough space on disk?

[vpymerel]

Hello,

Thank you for your answer,

There is several To available on the disk I am using right now

[chhylp123]

I see, thanks. How much fastq.gz do you have?

[vpymerel]

Only one

[chhylp123]

Haven' seen this issue before. What's the size of the fastq.gz file? From the log file, it seems it might be the disk issue. Can you check did hifiasm output *bin files?

[vpymerel]

The fastq.gz was 6Go,

I can't tell you if *bin files were output in failed runS because I am using hifiasm inside a snakemake pipeline that remove output folder when something is wrong,

However, a new run without a relative path as "-o" arg worked fine. I don't know if it may have been the problem,

Thank you

[chhylp123]

Does hifiasm work if you rerun -l3 with the new bin files? Thank you so much.

[oscarlr]

I get this error when the output directory doesn't exist. For example if the command is: "hifiasm -t 20 -o /user/results/out data.fastq.gz"

and if /user/results doesn't exist, then I get a segmentation fault.