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medvedevgroup / SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs
http://medvedevgroup.com/
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Error when using sbatch #26

Closed smallfade closed 3 years ago

smallfade commented 3 years ago

Hi,

I could get the sibeliaz command running fine on a node directly, but when I try to send the job using sbatch or snakemake --profile, I got errors. When use the sbatch the error is :

.conda/envs/sibeliaz/bin/sibeliaz: line 97: total_size + : syntax error: operand expected (error token is "+ ")
.conda/envs/sibeliaz/bin/sibeliaz: line 125: /usr/bin/time: No such file or directory
.conda/envs/sibeliaz/bin/sibeliaz: line 126: /usr/bin/time: No such file or directory

when use the snakemake --profile, the error is:

.snakemake_envs/3f9a8e3309e4f8576c8c3c7e6cd22727/bin/sibeliaz: line 131: /usr/bin/time: No such file or directory
.snakemake_envs/3f9a8e3309e4f8576c8c3c7e6cd22727/bin/sibeliaz: line 132: /usr/bin/time: No such file or directory

Maybe some hardcoded codes cause this error? How can I make SibeliaZ work with clusters?

smallfade commented 3 years ago

similar issue to https://github.com/medvedevgroup/SibeliaZ/issues/23