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AnantharamanLab / ViWrap

A wrapper to identify, bin, classify, and predict host-viral relationship for viruses
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Nanopore reads, no input files detected #34

Open jonbakerlab opened 8 months ago

jonbakerlab commented 8 months ago

Thanks for a great tool! Using v1.3.0, installed from GitHub, and this install seems to work fine when Illumina reads are used as input.

When I provide Nanopore reads as the input, 1) the flag --input_reads_type nanopore doesn't appear to be recognized:

$ /home/exacloud/gscratch/BakerLab/miniforge3/envs/viwrap_env/ViWrap/ViWrap run \
>     --input_metagenome 1.fasta \
>     --input_reads 1.fastq \
>     --out_dir 1_ont-ViWrap_out \
>     --db_dir /home/exacloud/gscratch/BakerLab/miniforge3/envs/viwrap_env/ViWrap/ViWrap_db \
>     --identify_method vb-vs \
>     --conda_env_dir /home/exacloud/gscratch/BakerLab/miniforge3/envs/viwrap_env/ \
>     --threads 36 \
>     --input_length_limit 5000 \
>     --input_reads_type nanopore
### Welcome to ViWrap ###

The issued command is:
/home/exacloud/gscratch/BakerLab/miniforge3/envs/viwrap_env/ViWrap/ViWrap run --input_metagenome 1.fasta --input_reads 1.fastq --out_dir 1_ont-ViWrap_out --db_dir /home/exacloud/
gscratch/BakerLab/miniforge3/envs/viwrap_env/ViWrap/ViWrap_db --identify_method vb-vs --conda_env_dir /home/exacloud/gscratch/BakerLab/miniforge3/envs/viwrap_env/ --threads 36 --
input_length_limit 5000

[2024-02-05 13:14:23] | Pre-check inputings. In processing...

and 2) I get the following error, looks like at the CoverM step:

$ cat slurm-24075205_3.out 
[2024-02-05T09:07:48Z INFO  coverm] CoverM version 0.6.1
[2024-02-05T09:07:48Z INFO  coverm] Using min-read-percent-identity 97%
[2024-02-05T09:08:31Z INFO  coverm] CoverM version 0.6.1
[2024-02-05T09:08:31Z INFO  coverm] Setting single read percent identity threshold at 0.97 for MetaBAT adjusted coverage, and not filtering out supplementary, secondary and improper pair alignments
[2024-02-05T09:08:31Z INFO  coverm] Using min-covered-fraction 0%
[2024-02-05T09:08:32Z INFO  coverm::contig] In sample '3.filtered', found 28387 reads mapped out of 28452 total (99.77%)

Error: No input files were identified. Verify that the input folder and extension are correct. Exiting.

Wondering if there is an issue with the input reads type not getting recognized, and it's looking for a 2nd input reads .fastq (i.e., as it would be for Illumina reads)?? Thanks in advance for your help!