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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Illegal instruction Error #517

Open bramdanneels opened 1 year ago

bramdanneels commented 1 year ago

Hi,

I'm trying to run hifiasm and get the following error using hifiasm 0.19.6:

Reads has been loaded. Loading ma_hit_ts from disk... ma_hit_ts has been read. Loading ma_hit_ts from disk... ma_hit_ts has been read. [M::ha_assemble::0.270*0.01] ==> loaded corrected reads and overlaps from disk [M::ha_opt_update_cov_min] updated max_n_chain to 100 /usr/bin/bash: line 2: 516412 Illegal instruction (core dumped) /cluster/projects/nn8013k/opt/hifiasm-0.19.5/hifiasm -o /cluster/projects/nn8013k/results/species/Calluna_vulgaris/ddCalVulg5/results/assembly/assembly -t10 --h1 /cluster/projects/nn8013k/results/species/Calluna_vulgaris/ddCalVulg5/genomic_data/hic/07-Calvul-TM2206_S6_001_1.fastq.gz --h2 /cluster/projects/nn8013k/results/species/Calluna_vulgaris/ddCalVulg5/genomic_data/hic/07-Calvul-TM2206_S6_001_2.fastq.gz /cluster/projects/nn8013k/results/species/Calluna_vulgaris/ddCalVulg5/genomic_data/pacbio/filtered/concat.filt.fastq.gz

Running on a cluster using 10 nodes and 150GB of memory

Any idea what the issue might be?

sdind commented 11 months ago

Hi, I got the same error and cannot figure out the problem. Did you find a solution ?

bramdanneels commented 11 months ago

Hi,

I'm not sure what the exact error was, but it seemed to have something to do with specifying the path of the output directory and the input files. I don't think it likes having "/" in the output directory parameter, so I cd'ed in the directory and specified the output as -o assembly. Then I also changed the input parameters to relative paths instead of absolute paths.

I don't know if both changes were necessary, but it make it work in the end.

AlcaArctica commented 11 months ago

I had a similar problem. I also noticed that command hifiasm -o yMyxXan -t 38 /lustre/projects/dazzlerAssembly/test_hifi_snake/ccs/yMyxXan_ccs.fastq.gz 2> hifiasm.log did not work. However, hifiasm -o ymyxxan -t 38 /lustre/projects/dazzlerAssembly/test_hifi_snake/ccs/yMyxXan_ccs.fastq.gz 2> hifiasm.log worked. Seems there are plenty of restraints on the -o flag (no file paths, no capital letters...)