FileNotFoundError: [Errno 2] No such file or directory: '/home/user/ViWrap_conda_environments/example_datatest_metaG_ViWrap_out5/02_vRhyme_outdir/vRhyme_best_bins_fasta_CheckV_result/CheckV_quality_summary.txt'

[MAXzbh]

Thank you for your nice pipeline, but when I run the pipeline through the test file provided in Github, I am getting the following error messages showing checkv_quality_summary.txt is missing:

Traceback (most recent call last): File "/home/user/ViWrap_conda_environments/ViWrap/ViWrap/ViWrap", line 173, in <module> output = cli() File "/home/user/ViWrap_conda_environments/ViWrap/ViWrap/ViWrap", line 167, in cli args["func"](args) File "/home/user/ViWrap_conda_environments/ViWrap/ViWrap/scripts/master_run.py", line 440, in main scripts.module.parse_checkv_result(vRhyme_best_bin_CheckV_result, CheckV_quality_summary) File "/home/user/ViWrap_conda_environments/ViWrap/ViWrap/scripts/module.py", line 487, in parse_checkv_result f = open(outfile, "w") FileNotFoundError: [Errno 2] No such file or directory: '/home/user/ViWrap_conda_environments/example_datatest_metaG_ViWrap_out5/02_vRhyme_outdir/vRhyme_best_bins_fasta_CheckV_result/CheckV_quality_summary.txt'

My input was:
ViWrap run --input_metagenome /home/user/ViWrap_conda_environments/ViWrap/ViWrap/example_data/test_metaG.fasta --input_reads /home/user/ViWrap_conda_environments/ViWrap/ViWrap/example_data/reads_1.fastq.gz,/home/user/ViWrap_conda_environments/ViWrap/ViWrap/example_data/reads_2.fastq.gz --out_dir /home/user/ViWrap_conda_environments/example_datatest_metaG_ViWrap_out4 --db_dir /home/user/ViWrap_conda_environments/ViWrap_db --identify_method genomad --conda_env_dir /home/user/ViWrap_conda_environments --threads 32 --input_length_limit 5000

I downloaded checkv db v1.5. tar. gz from [https://portal.nersc.gov/CheckV/] again decompressed it, and then reconfigured the checkv database using export CHECKVDB=/path/to/checkv db under both Viwrap and Viwrap_CheckV models, but the issue still cannot be solved. However, when I attempted to run the Viwrap CheckV module alone (using: checkv end_to_end input_file.fna output_directory - t 16), it was successful, meaning that the checkV database should already be set up correctly.

I feel quite puzzled and don’t know how to continue, even though I am eagerly expecting to use this pipeline. Would you please give a hand to solve the problem? I would be very grateful.

[clementcoclet]

I encountered the same issue. I believe it occurred because ViWrap attempted to run CheckV on the binning output (vRhyme). However, if vRhyme fails to find any bins, CheckV returns an error due to the empty input file. I am still unsure how to either skip the binning step or proceed with the ViWrap script even when no bins are found...

[ChengzhuangChen]

We are also experiencing this type of problem, which should not be caused by checkV, and there is no problem with vRhyme's, but rather the fact that vRhyme uses all the parameters, and in the overlap_final.contigs file, the generated .ffn as well as the .ffa file is 0. (When using the vb-vs method)