issue during the example run

[solna]

I went into this issue during the example run. Could you give some suggestions on solving this? I followed exactly the instruction online for the installation.

[Tue Feb 12 14:40:34 2019]
Error in rule align_reads_to_prefilter_contigs:
jobid: 0
output: S005/sequence_alignment/alignment_to_prefilter_contigs.sam
log: S005/logs/assembly/post_process/align_reads_to_prefiltered_contigs.log
conda-env: /home/chage/Public/atlas_databases/conda_envs/83ee959a

RuleException:
CalledProcessError in line 394 of /home/chage/miniconda3/envs/metagenome-atlas/lib/python3.6/site-packages/atlas/rules/assemble.snakefile:
Command 'source activate /home/chage/Public/atlas_databases/conda_envs/83ee959a; set -euo pipefail;
bbwrap.sh nodisk=t ref=S005/assembly/S005_prefilter_contigs.fasta in1=S005/sequence_quality_control/S005_QC_R1.fastq.gz,S005/sequence_quality_control/S005_QC_se.fastq.gz in2=S005/sequence_quality_control/S005_QC_R2.fastq.gz,null trimreaddescriptions=t out=S005/sequence_alignment/alignment_to_prefilter_contigs.sam threads=4 pairlen=1000 pairedonly=t minid=0.76 mdtag=t xstag=fs nmtag=t sam=1.3 local=t ambiguous=all secondary=t saa=f append=t machineout=t maxsites=10 -Xmx3G 2> S005/logs/assembly/post_process/align_reads_to_prefiltered_contigs.log ' returned non-zero exit status 1.
File "/home/chage/miniconda3/envs/metagenome-atlas/lib/python3.6/site-packages/atlas/rules/assemble.snakefile", line 394, in __rule_align_reads_to_prefilter_contigs
File "/home/chage/miniconda3/envs/metagenome-atlas/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Exiting because a job execution failed. Look above for error message
[Tue Feb 12 14:40:35 2019]
Finished job 6.
30 of 103 steps (29%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Note the path to the log file for debugging.
Documentation is available at: https://metagenome-atlas.readthedocs.io
Issues can be raised at: https://github.com/metagenome-atlas/atlas/issues
Complete log: /home/chage/Documents/atlas/.snakemake/log/2019-02-12T142818.012047.snakemake.log
[2019-02-12 14:40 CRITICAL] Command 'snakemake --snakefile /home/chage/miniconda3/envs/metagenome-atlas/lib/python3.6/site-packages/atlas/Snakefile --directory /home/chage/Documents/atlas --printshellcmds --jobs 8 --rerun-incomplete --configfile '/home/chage/Documents/atlas/config2.yaml' --nolock --use-conda --conda-prefix /home/chage/Public/atlas_databases/conda_envs all ' returned non-zero exit status 1.

[SilasK]

Hi @solna ,
The example_data is not ideal. It won't pass the binning.
It should however pass trough the assemlby step. atlas assemble

I assume it doesn't work for you with only 3G of memory. The alligning step is relatively memory demanding, ~30G.

You can also have a look at the log file: S005/logs/assembly/post_process/align_reads_to_prefiltered_contigs.log

[solna]

Thanks a lot for the prompt reply. I just tried with another set of real raw data on a workstation and it worked well. However I went into the same issue #29 as you mentioned with maxbin.

[SilasK]

This is not really a bug, it's more the sign that the assembly is too small.

• check the assembly report
  Possible solutions:
• use metabat (I think the best binner)
• use spades for assembly
  • when memory is a porblem you can deactivate the second error correction:
    by setting
    spades_skip_BayesHammer: true
    in the config file

[SilasK]

Have you used a snakemake profile, like this

[solna]

not yet, I will try to follow what you suggested above.
thanks a lot for the help.

[SilasK]

I think this issue is solved. Don't hesitate to re-open it.