jellyfish error when build database

[genostack]

when build databases jellyfish error on the first step and no other details .

Found jellyfish v1.1.12 Kraken build set to minimize disk writes. Found 12 sequence files (*.{fna,fa,ffn,fasta,fsa}) in the library directory. Creating k-mer set (step 1 of 6)... Using jellyfish xargs: cat: terminated by signal 13

is there any log output options I can get to debug this issue？

[MjelleLab]

Same here:

Found jellyfish v1.1.12 Kraken build set to minimize disk writes. Found 32502 sequence files (*.{fna,fa,ffn,fasta,fsa}) in the library directory. Creating k-mer set (step 1 of 6)... Using jellyfish Hash size not specified, using '50539588233' terminate called after throwing an instance of 'jellyfish::invertible_hash::ErrorAllocation' what(): Failed to allocate 353414451816 bytes of memory anaconda3/envs/krakenuniq/libexec/build_db.sh: line 46: 24475 Aborted jellyfish count -m 31 -s 50539588233 -C -t 20 -o database /dev/fd/63 xargs: cat: terminated by signal 13

[tanya-karagiannis]

I am running into a similar issue. Is there any suggestion how to resolve this?

Found jellyfish v1.1.12 Kraken build set to minimize disk writes. Found 49180 sequence files (*.{fna,fa,ffn,fasta,fsa}) in the library directory. Creating k-mer set (step 1 of 6)... Using jellyfish /usr3/graduate/sibald/.conda/envs/krakenuniq/libexec/build_db.sh: line 46: 777473 Aborted
jellyfish count -m 31 -s 178519674107 -C -t 16 -o database /dev/fd/63 xargs: cat: terminated by signal 13

[tanya-karagiannis]

I resolved this issue by loading the GCC compiler and adding the --jellyfish-bin argument. However, I now ran into a new issue with permission denied.

Code:

krakenuniq-build --db $DBNAME --kmer-len 31 --threads 16 --taxids-for-genomes --taxids-for-sequences --jellyfish-bin /restricted/projectnb/uh2-sebas/analysis/metagenomics/tanya_analyses/conda_envs/metagenomics/bin/jellyfish 

Error message: Kraken build set to minimize disk writes. Found 49180 sequence files (*.{fna,fa,ffn,fasta,fsa}) in the library directory. Creating k-mer set (step 1 of 6)... Using /restricted/projectnb/uh2-sebas/analysis/metagenomics/tanya_analyses/conda_envs/metagenomics/bin/jellyfish Hash size not specified, using '45303698809' /restricted/projectnb/uh2-sebas/analysis/metagenomics/tanya_analyses/conda_envs/metagenomics/share/krakenuniq-1.0.4-1/libexec/build_db.sh: line 45: database-build.log: Permission denied