Reassembly module stop without showing error

[rpeguil]

Hi,
I'm trying since several day to run the reassembly module on my refined bins but every time the job exits without any obvious error.
I'm working under linux system on a HPC and I submit my command line as a LSF job to the cluster. I'm using metawrap_1.3.
I first thought it was a memory problem but I have specified 40GB in the command line and in the resources asked to the cluster, and the issue persist.

Here my command line:
metawrap reassemble_bins -o /work3/rappe/Enrichement/New_MAGs/binning/BIN_REASSEMBLY -1 /work3/rappe/Enrichement/New_MAGs/trimData/all_reads/all_1.fastq -2 /work3/rappe/Enrichement/New_MAGs/trimData/all_reads/all_2.fastq -t 20 -m 40 -c 70 -x 5 -b /work3/rappe/Enrichement/New_MAGs/binning/BIN_REFINEMENT2/metawrap_70_10_bins

From this last command I obtained the two attached error and log files.
It seems to stop without showing error at the step "Aligning all reads back to entire assembly and splitting reads into individual fastqfiles based on their bin membership"

When the job stop, I have 3 output directories "binned_assembly", "original_bins" and "reads_for_reassembly".

Thank you for your help.

Output_metawrap_reassembly40M.err.txt
Output_metawrap_reassembly40M.out.txt

[rpeguil]

Also, strangely, the 1st time I tried the reassemble_bins module, the job went until creating a "reassemblies" (full of tmp directories) and an empty "reassembled_bins" directories. I was with this comand line:
metawrap reassemble_bins -o /work3/rappe/Enrichement/New_MAGs/binning/BIN_REASSEMBLY -1 /work3/rappe/Enrichement/New_MAGs/trimData/all_reads/all_1.fastq -2 /work3/rappe/Enrichement/New_MAGs/trimData/all_reads/all_2.fastq -t 30 -c 70 -x 5 -b /work3/rappe/Enrichement/New_MAGs/binning/BIN_REFINEMENT2/metawrap_70_5_bins

I tried to re-run the command line to finish this 1st analyses and here are the attached files.

Output_metawrap_reassembly40M_bis.err.txt
Output_metawrap_reassembly40M_bis.out.txt

The "reassembled_bins" directory is still empty.

[yqy6611]

You can check SPAdes logs in reassemblies folder.

[rpeguil]

Thank you for the comment.
I realised that most of the folders in "reassemblies" directory are empty. Only bin.1.permissive and bin.1.strict are containing files. I attach here the two SPAdes log files.
It seems like SPAdes finished the reassemblies but with a warning, and I'm not sure to understand it.
I still don't see the problem and why SPAdes suddenly stopped after doing 2 reassemblies "successfully".

spades_bin.1.permissive.log.txt
spades_bin.1.strict.log.txt

[yqy6611]

Seems like these two are okay. Did you check reads_for_reassembly folder?

[rpeguil]

Yes. In the reads_for_reassembly folder I have 4 files for each bin, with permissive and strict, _1 and _2. The files are not empty.

[yqy6611]

Then maybe pick one pair of reads in reads_for_reassembly uncapable to reassemble by metaWRAP and run SPAdes to target the issue.

[rpeguil]

Thank you for your advise!
In the meantime, I tried removing the --careful flag from the SPAdes command line in /envs/metawrap_1.3/bin/metawrap-modules/reassemble_bins.sh, as advised in issue #367 .
This seems to be working, as my job has now been running for over 24h for the first time. And the folders in reassemblies seem to be filling up.