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
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.
Here is my yaml file.
And here is the script I am running