VS2 issue

[drob2727]

ViWrap run --input_metagenome /home/fslcollab273/nobackup/archive/SALSA_Assembly/SALSA_ASSEMBLY/final_assembly.fasta
--input_reads /home/fslcollab273/nobackup/archive/SALSA_Assembly/ALL_SLM_SLM_BON_QC_READS/SLMCELL_1.fastq,/home/fslcollab273/nobackup/archive/SALSA_Assembly/ALL_SLM_SLM_BON_QC_READS/SLMCELL_2.fastq
--out_dir ./ViWrapTest_DR
--db_dir /home/fslcollab273/fsl_groups/grp_metawrap/nobackup/archive/ViWrap_DR/ViWrap_db
--identify_method vs
--conda_env_dir /home/fslcollab273/.conda/envs
--threads 128
--virome
--input_length_limit 5000

Welcome to ViWrap

The issued command is:
/home/fslcollab273/fsl_groups/grp_metawrap/nobackup/archive/ViWrap_DR/ViWrap-1.3.0/ViWrap run --input_metagenome /home/fslcollab273/nobackup/archive/SALSA_Assembly/SALSA_ASSEMBLY/final_assembly.fasta --input_reads /home/fslcollab273/nobackup/archive/SALSA_Assembly/ALL_SLM_SLM_BON_QC_READS/SLMCELL_1.fastq,/home/fslcollab273/nobackup/archive/SALSA_Assembly/ALL_SLM_SLM_BON_QC_READS/SLMCELL_2.fastq --out_dir ./ViWrapTest_DR --db_dir /home/fslcollab273/fsl_groups/grp_metawrap/nobackup/archive/ViWrap_DR/ViWrap_db --identify_method vs --conda_env_dir /home/fslcollab273/.conda/envs --threads 128 --virome --input_length_limit 5000

[2024-09-19 20:03:39] | Pre-check inputings. In processing...
[2024-09-19 20:08:40] | Looks like the input metagenome and reads, database, and custom MAGs dir (if option used) are now set up well, start up to run ViWrap pipeline
[2024-09-19 20:08:40] | Run VirSorter2 to identify viruses from input metagenome. Also plus CheckV to QC and trim, and KEGG, Pfam, and VOG HMMs to annotate viruses. In processing...
[2024-09-19 20:09:39] | Run VirSorter2 to identify viruses from input metagenome. Finished
[2024-09-19 20:09:41] | Run CheckV to QC and trim viruses identified from VirSorter2. Finished
Traceback (most recent call last):
File "/home/fslcollab273/fsl_groups/grp_metawrap/nobackup/archive/ViWrap_DR/ViWrap-1.3.0/ViWrap", line 173, in
output = cli()
File "/home/fslcollab273/fsl_groups/grp_metawrap/nobackup/archive/ViWrap_DR/ViWrap-1.3.0/ViWrap", line 167, in cli
args"func"
File "/nobackup/archive/grp/grp_metawrap/ViWrap_DR/ViWrap-1.3.0/scripts/master_run.py", line 179, in main
scripts.module.screen_virsorter2_result(args['virsorter_outdir'], keep1_list_file, keep2_list_file, discard_list_file, manual_check_list_file)
File "/nobackup/archive/grp/grp_metawrap/ViWrap_DR/ViWrap-1.3.0/scripts/module.py", line 2096, in screen_virsorter2_result
with open(final_viral_score, 'r') as lines:
FileNotFoundError: [Errno 2] No such file or directory: './ViWrapTest_DR/00_VirSorter_final_assembly/pass/final-viral-score.tsv'

[Drob84761]

Why would VS2 be running through the assembly in 1 minute? I installed everything according to the instructions and had no issues but running the software is not working. I have previously ran VS2 on this assembly and got 1200 viromes over 5000 bp. I used this one to test because my other dataset was getting the same issue. I am running this on a sbatch script if that helps.

[yyyangzd]

Did you solve the problem? I have the same problem too.

[Drob84761]

No I haven't yet. Ive been working on it for days. I think the issue is with the master set up script. My conda environments are so much smaller than what they are supposed to be. I have ran the set-up with every variation I can think of. Im out of ideas.

[try-hunter]

You can check if there is a yaml file and the corresponding conda environment in the conda_env file under the vs section in your database. This issue troubled me for a long time, until I discovered that the size of my database download was incorrect, and the conda environment was missing.

[brilliant2643]

You can check if there is a yaml file and the corresponding conda environment in the conda_env file under the vs section in your database. This issue troubled me for a long time, until I discovered that the size of my database download was incorrect, and the conda environment was missing.

Hi! I have the same problem when running viwrap with all the identify method, I manually install all the environments with yaml files and all the databases for the environments. How can I check if I download and set up the environments and databases correctly? Thanks a lot!

[try-hunter]

You can check if there is a yaml file and the corresponding conda environment in the conda_env file under the vs section in your database. This issue troubled me for a long time, until I discovered that the size of my database download was incorrect, and the conda environment was missing.

Hi! I have the same problem when running viwrap with all the identify method, I manually install all the environments with yaml files and all the databases for the environments. How can I check if I download and set up the environments and databases correctly? Thanks a lot!

You can use conda env list to check whether the conda environment was successfully installed. As for the database, since the author didn't provide MD5 checksums for verification, you can try using theducommand to check the storage size of each database and see if it roughly matches the size provided by the author.

[brilliant2643]

You can check if there is a yaml file and the corresponding conda environment in the conda_env file under the vs section in your database. This issue troubled me for a long time, until I discovered that the size of my database download was incorrect, and the conda environment was missing.

Hi! I have the same problem when running viwrap with all the identify method, I manually install all the environments with yaml files and all the databases for the environments. How can I check if I download and set up the environments and databases correctly? Thanks a lot!

You can use conda env list to check whether the conda environment was successfully installed. As for the database, since the author didn't provide MD5 checksums for verification, you can try using theducommand to check the storage size of each database and see if it roughly matches the size provided by the author.

Thanks for your reply! I tried conda env list command, and found all the environments were successfully installed, still when I run the command, I got errors. As for the du command, I tried and found the size of databases and environments path are all larger or smaller than the one listed in README file. I'm so confused.