Error in rule merge_assembly_cap3 - segmentation fault
Bug report
IMP3 stopped at the step of merge_assembly_cap3 without generating any content in the corresponding log file, but the screen message shown below:
Error in rule merge_assembly_cap3: jobid: 9 output: Assembly/mg.assembly.merged.fa log: logs/assembly_merge_assembly_cap3.log (check log file(s) for error message) conda-env: /users/jcnavarro/conda/e7a8faf3f71c32a40cabb702d36f2415 shell:
NAME_fin=Assembly/mg.assembly
NAME=Assembly/intermediary/mg.assembly
cat Assembly/intermediary/mg.megahit_preprocessed.1.fa Assembly/intermediary/mg.megahit_unmapped.2.fa > $NAME.cat.fa
# Run cap3
cap3 $NAME.cat.fa -p 98 -o 100 > logs/assembly_merge_assembly_cap3.log 2>&1
# Concatenate assembled contigs, singletons and rename the contigs
cat $NAME.cat.fa.cap.contigs $NAME.cat.fa.cap.singlets | awk '/^>/{print ">T111_contig_" ++i; next}{print}' > $NAME_fin.merged.fa
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /mnt/san.ese/nfs/users/jcnavarro/.snakemake/log/2021-11-23T110427.419676.snakemake.log
Log files and screenshots
see attachments
(List of logs/screenshots)
Steps to reproduce
I run IMP3 with an smaller dataset and it run well.
Code version
commit hash
branch name
Config files
2021-11-23T110427.419676.snakemake.log
sample.config.yaml (List of config files)
Command
# command used to launch IMP3
snakemake -s /users/jcnavarro/IMP3/Snakefile --configfile /users/jcnavarro/playing.yaml --use-conda --conda-prefix /users/jcnavarro/conda/ --cores 20
Input
R1/R2 fastq.gz for the metagenome of a soil sample. Each has a size of 20 Gb when compressed.
System
PRETTY_NAME="Debian GNU/Linux 10 (buster)" NAME="Debian GNU/Linux" VERSION_ID="10" VERSION="10 (buster)" VERSION_CODENAME=buster ID=debian HOME_URL="https://www.debian.org/" SUPPORT_URL="https://www.debian.org/support" BUG_REPORT_URL="https://bugs.debian.org/" MemTotal: 528365004 kB Threads/core: 64
Possible fixes
(Optional: How to fix)