Segmentation fault translatenucs

[sarah872]

Hi, I am running into the following error:

extractorfs /tmp/slurm-7400926/tmp/15758272862975753372/nucl_reads /tmp/slurm-7400926/tmp/15758272862975753372/nucl_6f_start --min-length 20 --max-length 45 --max-gaps 0 --contig-start-mode 1 --contig-end-mode 0 --orf-start-mode 0 --forward-frames 1,2,3 --reverse-frames 1,2,3 --translation-table 1 --use-all-table-starts 0 --id-offset 0 --threads 8 --compressed 0 -v 3

[=================================================================] 31.46M 23s 943ms
Time for merging files: 0h 0m 0s 423ms
Time for merging files: 0h 0m 0s 521ms
Time for processing: 0h 0m 31s 724ms
translatenucs /tmp/slurm-7400926/tmp/15758272862975753372/nucl_6f_start /tmp/slurm-7400926/tmp/15758272862975753372/aa_6f_start --translation-table 1 --add-orf-stop 1 -v 3 --compressed 0 --threads 8

[=================================================================] 944.07K 0s 331ms
Time for merging files: 0h 0m 0s 515ms
Time for processing: 0h 0m 1s 97ms
extractorfs /tmp/slurm-7400926/tmp/15758272862975753372/nucl_reads /tmp/slurm-7400926/tmp/15758272862975753372/nucl_6f_long --min-length 45 --max-length 32734 --max-gaps 0 --contig-start-mode 2 --contig-end-mode 2 --orf-start-mode 0 --forward-frames 1,2,3 --reverse-frames 1,2,3 --translation-table 1 --use-all-table-starts 0 --id-offset 0 --threads 8 --compressed 0 -v 3

[=================================================================] 31.46M 22s 660ms
Time for merging files: 0h 0m 0s 0ms
Time for merging files: 0h 0m 0s 0ms
Time for processing: 0h 0m 28s 889ms
tmp/15758272862975753372/assembler.sh: line 62: 31039 Segmentation fault      "$MMSEQS" translatenucs "${TMP_PATH}/nucl_6f_long" "${TMP_PATH}/aa_6f_long" ${TRANSLATENUCS_PAR}
Error: translatenucs long step died

[milot-mirdita]

What's the average length of your reads? Plass has a problem with too short reads.

You can adjust the minimum protein fragment extraction length with the --min-length parameter. plass assemble --min-length 15 will extract protein fragments of at least length 15 which should still work with 75bp long reads.

[sarah872]

Read length is 80 after trimming. Adding the --min-length 15 parameter worked. Thank you!