Open Edison2021 opened 2 years ago
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
@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.
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.
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
Thank you for the feedback. I'm starting to work on the fixes.
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
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "CRISPRidentify.py", line 249, in
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
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
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