jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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The pipeline stopped without finishing megahit #745

Closed feixiang1209 closed 8 months ago

feixiang1209 commented 8 months ago

After almost 24 hours, the analysis stopped. Please see below error message. Can you please help?

Error running command: /home/zhaox0b/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/megahit/megahit -1 /home/zhaox0b/metagenomics/test2/test2/data/raw_fastq/par1.fastq.gz -2 /home/zhaox0b/metagenomics/test2/test2/data/raw_fastq/par2.fastq.gz -t 12 -o /home/zhaox0b/metagenomics/test2/test2/data/megahit >> /home/zhaox0b/metagenomics/test2/test2/syslog 2>&1 at /home/zhaox0b/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl line 36. Assembly not present in /home/zhaox0b/metagenomics/test2/test2/results/01.test2.fasta, exiting Stopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally

If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /home/zhaox0b/metagenomics/test2/test2/syslog file (zip it first) Died at /home/zhaox0b/miniconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 941.

feixiang1209 commented 8 months ago

syslog.zip

Upload the syslog file. Thanks

fpusan commented 8 months ago

Exit code -9 means that the process was killed, probably because it exceeded the memory limit. If running on a computing cluster, please allocate more memory to the job.