vRhyme_nucmer_delta_parsed.tsv not found

[XiongGZ]

Version: Version 1.1.0 (March 2022)

Command: vRhyme -t 28 --method longest -i $Assemble/final.contigs.fa -g $Gene_predict/nucl.fa -p $Gene_predict/prot.fa -r $Binning/trimmed_1.fastq $Binning/trimmed_2.fastq -o $Binning/vrhyme

Error report:
Traceback (most recent call last): File "/home/xiongguangzhou/Software/miniconda3/envs/vrhyme/bin/vRhyme", line 541, in <module> code, original, sequences = derep_stuff.derep_stuff_longest(in_fasta, int(threads), interest_list, folder, base, derep_len, nuc_c, nuc_b, nuc_g, nuc_split, derep_id, derep_frac, sketch_k, sketch_s, iterations) File "/home/xiongguangzhou/Software/miniconda3/envs/vrhyme/bin/derep_stuff.py", line 852, in derep_stuff_longest clusters_100_dict, original_seqs, _ = nucmer_filter_1_stuff(original_seqs, folder) File "/home/xiongguangzhou/Software/miniconda3/envs/vrhyme/bin/derep_stuff.py", line 327, in nucmer_filter_1_stuff with open(folder + "vRhyme_dereplication/vRhyme_nucmer_delta_parsed.tsv", "r") as coords: FileNotFoundError: [Errno 2] No such file or directory: '/data4/xiongguangzhou/01.Soil/Metagenome/1-1/05.Binning/vrhyme/vRhyme_dereplication/vRhyme_nucmer_delta_parsed.tsv'

Can you help me?
Thanks!

[KrisKieft]

Please check out Issue #2 for a potential solution.

[XiongGZ]

After i remove --method, a new error report

Command:
vRhyme -t 48 --model hybrid --method none -i $Virus_identify/virus.contigs.fa -g $Gene_predict/nucl.fa -p $Gene_predict/prot.fa -r $Binning/Trimmed_1.fastq $Binning/Trimmed_2.fastq -o $Binning/vrhyme

Error report:

cat: /data4/xiongguangzhou/01.Soil/Metagenome/1-1/05.Binning/vrhyme/vRhyme_sam_files/Trimmed_1.sam: No such file or directory
rm: cannot remove ‘/data4/xiongguangzhou/01.Soil/Metagenome/1-1/05.Binning/vrhyme/vRhyme_sam_files/Trimmed_1.sam’: No such file or directory

Error. No file(s) for coverage information were identified. Check coverage inputs (c/b/s/r/u/v). Exiting.

There was no output in vRhyme_sam_files directory.
It seems the alignment process did not work.

Test the Installation
test_vRhyme.py (test run)

  Python Dependencies
  -------------------
  scikit-learn: Success (v1.1.1)
  numpy: Success (v1.22.4)
  numba: Success (v0.55.2)
  pandas: Success (v1.4.2)
  pysam: Success (v0.19.1)
  networkx: Success (v2.8.4)


  Program Dependencies
  --------------------
  mmseqs: Success
  samtools: Success  prodigal: Success
  mash: Success
  nucmer: Success
  bowtie2: Success
  bwa: Success


  Machine Learning Models
  -----------------------
  NN model: Success
  ET model: Success