Error running dammit annotation

[prvasquez]

When I try to run the annotation pipeline I keep getting this error. I think it has to do with calling a user-database. I have a fasta file that I want to use for annotation.

Here is the dammit log.

ty.fasta.dammit/shark_trinity.fasta -m 80`
- [x] TransDecoder.Predict:shark_trinity.fasta: 
    * Cmd: `/pylon5/mc5phkp/pvasquez/projects/shark/.snakemake/conda/f82fdf1a/bin/TransDecoder.Predict -t /pylon5/mc5phkp/pvasquez/projects/shark/out/shark_out/annotation/shark_trinity.fasta.dammit/shark_trinity.fasta`
- [ ] user-database:proteins_from_10kbp_scaffolds.fasta-shmlast-rename:/pylon5/mc5phkp/pvasquez/projects/shark/out/shark_out/annotation/shark_trinity.fasta.dammit/shark_trinity.fasta: 
    * Python: function setup_profiler.add_profile_actions.start_profiling
    * Python: rename_input
    * Python: function setup_profiler.add_profile_actions.stop_profiling
- [ ] user-database:proteins_from_10kbp_scaffolds.fasta-shmlast-rename:/pylon5/mc5phkp/pvasquez/elvers/dammit_databases/shark/proteins_from_10kbp_scaffolds.fasta: 
    * Python: function setup_profiler.add_profile_actions.start_profiling
    * Python: rename_input
    * Python: function setup_profiler.add_profile_actions.stop_profiling
TaskError - taskid:user-database:proteins_from_10kbp_scaffolds.fasta-shmlast-rename:/pylon5/mc5phkp/pvasquez/elvers/dammit_databases/shark/proteins_from_10kbp_scaffolds.fasta
PythonAction Error
Traceback (most recent call last):
  File "/pylon5/mc5phkp/pvasquez/projects/shark/.snakemake/conda/f82fdf1a/lib/python3.7/site-packages/doit/tools.py", line 218, in execute
    returned_value = self.py_callable(*self.args, **kwargs)
  File "/pylon5/mc5phkp/pvasquez/projects/shark/.snakemake/conda/f82fdf1a/lib/python3.7/site-packages/shmlast/translate.py", line 114, in rename_input
    for n, record in enumerate(screed.open(input_fn)):
  File "/pylon5/mc5phkp/pvasquez/projects/shark/.snakemake/conda/f82fdf1a/lib/python3.7/site-packages/screed/openscreed.py", line 39, in __init__
    self.iter_fn = self.open_reader(filename, *args, **kwargs)
  File "/pylon5/mc5phkp/pvasquez/projects/shark/.snakemake/conda/f82fdf1a/lib/python3.7/site-packages/screed/openscreed.py", line 56, in open_reader
    bufferedfile = io.open(file=filename, mode='rb', buffering=8192)
FileNotFoundError: [Errno 2] No such file or directory: '/pylon5/mc5phkp/pvasquez/elvers/dammit_databases/shark/proteins_from_10kbp_scaffolds.fasta'

########################################
TaskError - taskid:user-database:proteins_from_10kbp_scaffolds.fasta-shmlast-rename:/pylon5/mc5phkp/pvasquez/elvers/dammit_databases/shark/proteins_from_10kbp_scaffolds.fasta
user-database:proteins_from_10kbp_scaffolds.fasta-shmlast-rename:/pylon5/mc5phkp/pvasquez/elvers/dammit_databases/shark/proteins_from_10kbp_scaffolds.fasta <stderr>:

user-database:proteins_from_10kbp_scaffolds.fasta-shmlast-rename:/pylon5/mc5phkp/pvasquez/elvers/dammit_databases/shark/proteins_from_10kbp_scaffolds.fasta <stdout>:

Here is my yaml file.

# nema: a non-random subset of data from Tulin et al. (2013), that can
# be used to do assembly and comparative expression analysis.

# this sets the output directory name:
basename: 'shark'

get_data:
  # this says to download samples specified as Web URLs:
  # this describes the samples:
  samples: "/pylon5/mc5phkp/pvasquez/projects/shark/shark.samples.csv"

out_path: /pylon5/mc5phkp/pvasquez/projects/shark/out

dammit:
  busco_group:     # specify all busco groups below here
  - metazoa
  - eukaryota
  db_dir: /pylon5/mc5phkp/pvasquez/elvers/dammit_databases/   # specify location for databases (or previously installed databases)
  db_install_only: False   # just install databases, don't run annotation
  db_extra: ''
  annot_extra: '--quick --user-databases /pylon5/mc5phkp/pvasquez/elvers/dammit_databases/shark/proteins_from_10kbp_scaffolds.fasta'

trimmomatic:
  adapter_file:
    pe_path: /pylon5/mc5phkp/pvasquez/projects/shark/TruSeq2-PE.fa
    se_path: ep_utils/TruSeq3-SE.fa
  trim_cmd: ILLUMINACLIP:{}:2:40:15 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:35
  extra: '' 

khmer:
  C: 3
  Z: 18
  coverage: 20
  diginorm: true
  extra: ''
  ksize: 20
  memory: 4e9

trinity:
  add_single_to_paired: false
  input_kmer_trimmed: true
  input_trimmomatic_trimmed: false
  max_memory: 1000G
  seqtype: fq
  extra: '--CPU 32'

workflows:
  - annotate

And here is the script I am running

#!/bin/bash -l
#SBATCH -D /pylon5/mc5phkp/pvasquez/projects/shark/
#SBATCH -J shark_default
#SBATCH -o /pylon5/mc5phkp/pvasquez/slurm/out/shark_annotate.txt
#SBATCH -e /pylon5/mc5phkp/pvasquez/slurm/err/shark_annotate.txt
#SBATCH -t 8:00:00
#SBATCH -p RM-small
#SBATCH -N 1
#SBATCH --ntasks-per-node=8
#SBATCH -C EGRESS

conda activate elvers-env

cd /pylon5/mc5phkp/pvasquez/projects/shark

elvers shark.yaml assemble annotate

[prvasquez]

I had an error in one my paths that was causing the issue. I fixed it and it worked.