[BUG] Error in rule megahit

[PeymanDerik]

Short description of the problem

CalledProcessError in file /Snakefile, line 632.

anvi'o version

Anvi'o .......................................: marie (v8) Python .......................................: 3.10.15

Profile database .............................: 38 Contigs database .............................: 21 Pan database .................................: 16 Genome data storage ..........................: 7 Auxiliary data storage .......................: 2 Structure database ...........................: 2 Metabolic modules database ...................: 4 tRNA-seq database ............................: 2

System info

I use Linux 64-bit Installed Anvio using: "pip install anvio-8.tar.gz"

Detailed description of the issue

I get this error when running command "anvi-run-workflow -w metagenomics -c config-megahit.json --additional-params --cores 24 --keep-going --rerun-incomplete":

Error in rule megahit: jobid: 0 input: 01_QC_megahit/S00JY_0368-QUALITY_PASSED_R1.fastq.gz, 01_QC_megahit/S00JY_0506-QUALITY_PASSED_R1.fastq.gz, 01_QC_megahit/S00JY_0368-QUALITY_PASSED_R2.fastq.gz, 01_QC_megahit/S00JY_0506-QUALITY_PASSED_R2.fastq.gz output: 02_FASTA_megahit/Kinsella Tame 2A/final.contigs.fa log: 00_LOGS_megahit/Kinsella Tame 2A-megahit.log (check log file(s) for error details)

RuleException: CalledProcessError in file /gpfs/fs3c/aafc/aafc_shp/pdv000/Anvio/anvio-8/lib/python3.10/site-packages/anvio/workflows/metagenomics/Snakefile, line 632: Command 'set -euo pipefail; megahit -1 01_QC_megahit/S00JY_0368-QUALITY_PASSED_R1.fastq.gz,01_QC_megahit/S00JY_0506-QUALITY_PASSED_R1.fastq.gz -2 01_QC_megahit/S00JY_0368-QUALITY_PASSED_R2.fastq.gz,01_QC_megahit/S00JY_0506-QUALITY_PASSED_R2.fastq.gz -o 02_FASTA_megahit/Kinsella Tame 2A_TEMP -t 24 --min-contig-len 1000 --memory 1000000.0 >> 00_LOGS_megahit/Kinsella Tame 2A-megahit.log 2>&1' returned non-zero exit status 127. File "/gpfs/fs3c/aafc/aafc_shp/pdv000/Anvio/anvio-8/lib/python3.10/site-packages/anvio/workflows/metagenomics/Snakefile", line 632, in __rule_megahit File "/gpfs/fs3c/aafc/aafc_shp/pdv000/Anvio/anvio-8/lib/python3.10/concurrent/futures/thread.py", line 58, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Exiting because a job execution failed. Look above for error message

[ivagljiva]

Hi @PeymanDerik,

Installed Anvio using: "pip install anvio-8.tar.gz"

If the pip install is the only command you used to install anvi'o, then that is probably the issue. You need to follow all the instructions at https://anvio.org/install/linux/stable/ to make sure you have all the required dependencies.

I suspect that is the case since your paths don't appear to make use of a conda environment :) Please re-install following the appropriate instructions.

[PeymanDerik]

Thanks. I followed all the instructions and then ran "conda install pulp=2.7" (because I was getting an error for this). I removed my Anvio and re-install it but I still get the same error!

[PeymanDerik]

I don't see megahit in my /bin and here is the output of megahit log: /usr/bin/bash: megahit: command not found. I would appreciate your guidance on this. Thanks!

[meren]

This means not everything worked during your installation, and anvi'o is not installed properly.

Please try again, @PeymanDerik. Or go through the installation instructions with a local bioinformatician to figure out what goes wrong.

[PeymanDerik]

I re-installed it three times and never got any error on that but the issue persists. Will try again. Thanks!

[meren]

Try again with someone beside you :) Something is going wrong somewhere and you are not realizing it, and repeating the same steps will unlikely help.

[PeymanDerik]

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done Executing transaction: / vmatch selection functions are installed in /gpfs/fs3c/aafc/aafc_shp/pdv000/Anvio/anvio-8/lib. You can use them without specifying their full path. Symbol map files are installed in /gpfs/fs3c/aafc/aafc_shp/pdv000/Anvio/anvio-8/share/vmatch-2.3.0-5/TRANS/. Activation and deactivation scripts will set MKVTREESMAPDIR accordingly so you can use symbol map files without specifying their full path. Those scripts are in /gpfs/fs3c/aafc/aafc_shp/pdv000/Anvio/anvio-8/etc/conda/activate.d/vmatch-2.3.0-5.sh and /gpfs/fs3c/aafc/aafc_shp/pdv000/Anvio/anvio-8/etc/conda/deactivate.d/vmatch-2.3.0-5.sh respectively.

| \ done

I will, thanks again!

[meren]

I'm sorry for not being able to help you more, @PeymanDerik. There are much easier tools out there that will likely be more than enough for your questions. I hope you will find a way to analyze your data and find in them the answers you are looking for :)

Best wishes, Meren