Premature ending without any error message

[jolespin]

Description of bug

Here's the command:

metaspades.py -o ../veba_output/assembly/LAM_Final_B5_1_sed_S5/intermediate/1__assembly --restart-from last --tmp-dir ../veba_output/assembly/LAM_Final_B5_1_sed_S5/tmp/assembly --threads 1 --memory 200

Basically, we tried to pick up from a previous run and the job stopped w/o an error message. We requested 48 hours of run time but the time got to 22:04:16.761 so I don't think it was a timeout issue.

It looks like K55 started:

(base) [jespinoz@exp-15-01 Commands]$ ls -lhS ../veba_output/assembly/LAM_Final_B5_1_sed_S5/intermediate/1__assembly/K55/configs/
total 136K
-rw-r--r-- 1 aphillip jcl122 6.9K Aug 21 18:15 simplification.info
-rw-r--r-- 1 aphillip jcl122 5.0K Aug 21 18:15 rna_mode.info
-rw-r--r-- 1 aphillip jcl122 5.0K Aug 21 18:15 config.info
-rw-r--r-- 1 aphillip jcl122 4.8K Aug 21 18:15 meta_mode.info
-rw-r--r-- 1 aphillip jcl122 4.3K Aug 21 18:15 pe_params.info
-rw-r--r-- 1 aphillip jcl122 2.2K Aug 21 18:15 moleculo_mode.info
-rw-r--r-- 1 aphillip jcl122 2.0K Aug 21 18:15 mda_mode.info
-rw-r--r-- 1 aphillip jcl122 1.4K Aug 21 18:15 distance_estimation.info
-rw-r--r-- 1 aphillip jcl122 1.1K Aug 21 18:15 metaviral_mode.info
-rw-r--r-- 1 aphillip jcl122 1019 Aug 21 18:15 detail_info_printer.info
-rw-r--r-- 1 aphillip jcl122  645 Aug 21 18:15 construction.info
-rw-r--r-- 1 aphillip jcl122  636 Aug 21 18:15 rnaviral_mode.info
-rw-r--r-- 1 aphillip jcl122  633 Aug 21 18:15 careful_mode.info
-rw-r--r-- 1 aphillip jcl122  564 Aug 21 18:15 careful_mda_mode.info
-rw-r--r-- 1 aphillip jcl122  551 Aug 21 18:15 plasmid_mode.info
-rw-r--r-- 1 aphillip jcl122  131 Aug 21 18:15 tsa.info
-rw-r--r-- 1 aphillip jcl122  126 Aug 21 18:15 large_genome_mode.info
-rw-r--r-- 1 aphillip jcl122  110 Aug 21 18:15 hmm_mode.info
-rw-r--r-- 1 aphillip jcl122   45 Aug 21 18:15 metaplasmid_mode.info
-rw-r--r-- 1 aphillip jcl122   44 Aug 21 18:15 isolate_mode.info
-rw-r--r-- 1 aphillip jcl122   43 Aug 21 18:15 toy.info

I'm trying to figure out if I should try to continue the jobs or use MEGAHIT (which I'd rather not use since many of the jobs got pretty far)

spades.log

spades.log.zip

params.txt

(base) [jespinoz@exp-15-01 Commands]$ cat ../veba_output/assembly/LAM_Final_B5_1_sed_S5/intermediate/1__assembly/params.txt Command line: /expanse/projects/jcl122/miniconda3/envs/VEBA-assembly_env/bin/metaspades.py -o /expanse/projects/jcl122/vesta/veba_output/assembly/LAM_Final_B5_1_sed_S5/intermediate/1__assembly -1 /expanse/projects/jcl122/vesta/veba_output/preprocess/LAM_Final_B5_1_sed_S5/output/cleaned_1.fastq.gz -2 /expanse/projects/jcl122/vesta/veba_output/preprocess/LAM_Final_B5_1_sed_S5/output/cleaned_2.fastq.gz --tmp-dir /expanse/projects/jcl122/vesta/veba_output/assembly/LAM_Final_B5_1_sed_S5/tmp/assembly --threads 1 --memory 128 --tmp-dir ../veba_output/assembly/LAM_Final_B5_1_sed_S5/tmp/assembly --threads 1 --memory 243 --tmp-dir ../veba_output/assembly/LAM_Final_B5_1_sed_S5/tmp/assembly --threads 1 --memory 200 Restart-from=last with updated parameters: --tmp-dir ../veba_output/assembly/LAM_Final_B5_1_sed_S5/tmp/assembly --threads 1 --memory 200

System information: SPAdes version: 3.15.5 Python version: 3.9.15 OS: Linux-4.18.0-477.15.1.el8_8.x86_64-x86_64-with-glibc2.28

Output dir: /expanse/projects/jcl122/vesta/veba_output/assembly/LAM_Final_B5_1_sed_S5/intermediate/1__assembly Mode: read error correction and assembling Debug mode is turned OFF

Dataset parameters: Metagenomic mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/expanse/projects/jcl122/vesta/veba_output/preprocess/LAM_Final_B5_1_sed_S5/output/cleaned_1.fastq.gz'] right reads: ['/expanse/projects/jcl122/vesta/veba_output/preprocess/LAM_Final_B5_1_sed_S5/output/cleaned_2.fastq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: [21, 33, 55] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /expanse/projects/jcl122/vesta/veba_output/assembly/LAM_Final_B5_1_sed_S5/tmp/assembly Threads: 1 Memory limit (in Gb): 200

SPAdes version

SPAdes v3.15.5

Operating System

Linux-4.18.0-477.15.1.el8_8.x86_64-x86_64-with-glibc2.28

Python Version

3.9.15

Method of SPAdes installation

conda

No errors reported in spades.log

• [X] Yes