FileNotFoundError: [Errno 2] No such file or directory: 'Host_prediction_to_genome_m90.csv'

[CynthiaChibani]

Hey There,
Thank you for providing a super cool pipeline.
I managed to get it to work with the recent genomad integration, but I got an error at one of the last steps of the pipeline.

My command line:

cd $WORK/ViWrap
./ViWrap run --input_metagenome ./CB_HGUT_timeseries_ViWrap/Metagenomes_ASSEMBLY/Sport1_TP1/final_assembly.fasta
--input_reads ./CB_HGUT_timeseries_ViWrap/Metagenomes_READ_QC/Sport1_TP1/final_pure_reads_1.fastq.gz,./CB_HGUT_timeseries_ViWrap/Metagenomes_READ_QC/Sport1_TP1/final_pure_reads_2.fastq.gz
--out_dir ./CB_HGUT_timeseries_ViWrap/ViWrap_Out/Sport1_TP1_Out
--db_dir ./ViWrap_db/
--identify_method genomad
--conda_env_dir $HOME/.conda/envs/ViWrap_new/
--threads 12
--virome
--input_length_limit 5000
--custom_MAGs_dir ./CB_HGUT_timeseries_ViWrap/MAGs/Sport1_TP1
--iPHoP_db_custom ./CB_HGUT_timeseries_ViWrap/iPHoP_db_custom/Sport1_TP1/

Error:

Traceback (most recent call last):
File "./ViWrap", line 173, in
output = cli()
File "./ViWrap", line 167, in cli
args"func"
File "$WORK/ViWrap/scripts/master_run.py", line 620, in main
scripts.module.combine_iphop_results(args, combined_host_pred_to_genome_result, combined_host_pred_to_genus_result)
File "$WORK/ViWrap/scripts/module.py", line 1845, in combine_iphop_results
with open(host_pred_to_genome_m90, 'r') as lines:
FileNotFoundError: [Errno 2] No such file or directory: '$WORK/CB_HGUT_timeseries_ViWrap/ViWrap_Out/Sport1_TP1_Out/07_iPHoP_outdir/Host_prediction_to_genome_m90.csv'

I would appreciate any input you might have.
Best,
Cynthia

[CynthiaChibani]

Hey there, I narrowed it down to an issue with RaFAH, perl: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory
I once solved it using the following:
cd $CONDA_PREFIX/lib
ln -s libnsl.so.3.0.0 libnsl.so.1

but it did not help in this situation, I tried to follow the issues raised here , but it does not seem I have Perl errors.

I installed iphop in a fresh micromamba env independent of ViWrap and it seems to have done the trick.

I can't figure out how to fix it in ViWrap, if you have ideas I would appreciate it :)

[ewars]

Hi.
I had a similar error. My problem was with the routes, try removing the / at the end of each route. Maybe it will help you