summary_identify.csv is missing

[Edison2021]

Hi Alex
I run a trial test and found an error as below:
Command
python3.7 CRISPRloci_standalone.py -f NC_005230.fasta -output NC_005230.fasta.dir -st dna -cpu 32
Final output
summary crispr Example/NC_005230.fasta.dir/summary_crisp.csv
dirname cas Example/NC_005230.fasta.dir/tmp/output-Casboundary/predictions/
This file does not exist: Example/NC_005230.fasta.dir/summary_identify.csv

Best
Edison

[Edison2021]

In addition, there is another error reported:
Error: Unable to access jarfile CRISPRloci_webserver_visualization/CRISPRloci_visualization.jar

I searched CRISPRloci folder but did not find the folder CRISPRloci_webserver_visualization.

Best
Edison

[niccw]

@Edison2021

I also encountered the same error. After checking, one of the biggest problems is that environments.yml miss packages that are required for CRISPRidentify.

[Alexander-Mitrofanov]

Thank you for submitting the problems.
The fixes will be applied at the beginning of April.
For the time being please try to use the CRISPRloci web interface.

[JPegorino]

just in case it is helpful for bug fixes, I'm getting (I think) related errors with this at the end of April (running on a complete reference genome from NCBI) and I thought I'd copy them here:

cp: cannot stat '/home/ubuntu/volume2/pangenome/MGEs/CRISPR_Cas/test/tmp/output-CRISPRidentify/GCA_000008485/CRISPR*': No such file or directory
cp: cannot stat '/home/ubuntu/volume2/pangenome/MGEs/CRISPR_Cas/test/tmp/output-CRISPRidentify/GCA_000008485/Spacers*': No such file or directory
This file does not exist: /home/ubuntu/volume2/pangenome/MGEs/CRISPR_Cas/test/tmp/output-Casboundary/predictions/
Error: Unable to access jarfile /home/ubuntu/software/CRISPRloci-1.0.0/CRISPRloci_webserver_visualization/CRISPRloci_visualization.jar
summary crispr /home/ubuntu/volume2/pangenome/MGEs/CRISPR_Cas/test/summary_crisp.csv
dirname cas /home/ubuntu/volume2/pangenome/MGEs/CRISPR_Cas/test/tmp/output-Casboundary/predictions/
summary crispr /home/ubuntu/volume2/pangenome/MGEs/CRISPR_Cas/test/summary_crisp.csv
dirname cas /home/ubuntu/volume2/pangenome/MGEs/CRISPR_Cas/test/tmp/output-Casboundary
This file does not exist: /home/ubuntu/volume2/pangenome/MGEs/CRISPR_Cas/test/summary_identify.csv

Many thanks,
Jamie

[Alexander-Mitrofanov]

Thank you for the feedback. I'm starting to work on the fixes.

[pjbiggs]

Hi,
I am wanting to run the code on hundreds of genomes. I am having a similar issue to those above, but I also note additional problems. When I ran the command for the first time, the 4 .tar.gz files were extracted for CASboundary. It did not find them automatically for CRISPRcasIdentifier. I extracted them manually and now have trained_models.tar.gz and HMM_sets.tar.gz in the CRISPRcasIdentifier folder along with their extracted folders. I also have the extracted folders in the root CRISPRloci-1.0.0 folder.
I am running the test command: python3.7 CRISPRloci_standalone.py -f Example/NC_005230.fasta -st dna -output test1 into a new results folder. My errors are as below:

`1. Run initial array detection
2. Refine detected arrays
3. Evaluate candidates
4. Enhance evaluated arrays
5. Complement arrays with additional info
Traceback (most recent call last):
File "components/module_non_array_computations.py", line 164, in _calculate_strand
st = StrandComputationNew(list_of_crisprs=self.list_of_crisprs_bona_fide)
File "components/components_non_array_computations.py", line 111, in init
self._compute_all_strands()
File "components/components_non_array_computations.py", line 134, in _compute_all_strands
with open("ResultsStrand/CRISPRstrand_Summary.tsv", "r") as f:
FileNotFoundError: [Errno 2] No such file or directory: 'ResultsStrand/CRISPRstrand_Summary.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "CRISPRidentify.py", line 249, in
run_over_one_file(complete_path_file, folder_result, pickle_folder)
File "CRISPRidentify.py", line 210, in run_over_one_file
flag_dev_mode=FLAG_DEVELOPER_MODE)
File "components/pipeline.py", line 32, in init
self._run_non_crispr_computation()
File "components/pipeline.py", line 75, in _run_non_crispr_computation
flag_dev_mode=self.flag_dev_mode)
File "components/module_non_array_computations.py", line 34, in init
self._calculate_all_non_array_values()
File "components/module_non_array_computations.py", line 46, in _calculate_all_non_array_values
self._calculate_strand()
File "components/module_non_array_computations.py", line 171, in _calculate_strand
st = StrandComputation(list_of_crisprs=self.list_of_crisprs_bona_fide)
File "components/components_non_array_computations.py", line 93, in init
self._compute_all_strands()
File "components/components_non_array_computations.py", line 98, in _compute_all_strands
strand = get_orientation(consensus)
File "components/components_non_array_computations.py", line 48, in get_orientation
f = open("prediction", "r")
FileNotFoundError: [Errno 2] No such file or directory: 'prediction'
Error: Unable to access jarfile /home/pbiggs/software/CRISPRloci-1.0.0/CRISPRloci_webserver_visualization/CRISPRloci_visualization.jar
summary crispr /home/pbiggs/software/CRISPRloci-1.0.0/test1/summary_crisp.csv
dirname cas /home/pbiggs/software/CRISPRloci-1.0.0/test1/tmp/output-Casboundary/predictions/
This file does not exist: /home/pbiggs/software/CRISPRloci-1.0.0/test1/summary_identify.csv`

I am running this in WSL2 using Ubuntu 20.04, and I have no issues with conda environments.
Any thoughts please on how to solve this?
Thanks,
Patrick

[Old-Green-Man]

Regarding the Readme example, as pjbiggs mentioned above, the tar archives in CRISPRcasIdentifier are not being auto extracted as indicated in the Readme.

Also, the example:

python3.7 CRISPRloci_standalone.py -f Example/NC_005230_proteins.fasta -st protein

should be

python3.7 CRISPRloci_standalone.py -f Example/NC_005230_proteins.fa -st protein

and I'm not seeing Example/Input3.fa for the virus example