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HIT-ImmunologyLab / DBSCAN-SWA

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Error parsing prophage feature value #7

Closed peng-ye closed 2 years ago

peng-ye commented 2 years ago

Dear Author,

Would you please help sort this error out? Thanks.

In the STDOUT: step7:start to annotate the predicted prophage regions parse prophage feature value error!

In the STDERR: # There is no *blastn* files in the _prophageannotation folder

Exception in thread Thread-5: Traceback (most recent call last): File "/home/pengye/Software/anaconda3/envs/prokka/lib/python3.7/threading.py", line 926, in _bootstrap_inner self.run() File "/home/pengye/Software/anaconda3/envs/prokka/lib/python3.7/threading.py", line 870, in run self._target(*self._args, **self._kwargs) File "/home/pengye/Software/DBSCAN-SWA/bin/dbscan-swa.py", line 1659, in parse_prophage_blastn_phagedb_6 with open(outfile) as f: FileNotFoundError: [Errno 2] No such file or directory: 'results/prophage_annotation/prophage_blastn_phage'

Traceback (most recent call last): File "/home/pengye/Software/DBSCAN-SWA/bin/dbscan-swa.py", line 2706, in predict_prophage(strain_id,inputfile_bac,outdir,add_annotation,prefix) File "/home/pengye/Software/DBSCAN-SWA/bin/dbscan-swa.py", line 2574, in predict_prophage visualize(save_prophage_file,save_prophage_nucl_file,save_prophage_protein_file,prophage_region_annotate_dir,add_annotation,templeate_file,save_html_file) File "/home/pengye/Software/DBSCAN-SWA/bin/dbscan-swa.py", line 2356, in visualize with open(prophage_hit_phage_file) as f: FileNotFoundError: [Errno 2] No such file or directory: 'results/prophage_annotation/prophage_annotate_phage_details.txt'

gancao commented 2 years ago

Hello, @peng-ye

Could you please provide the sequence file that met the error of it is convenient? or you can give me a screenshot of the results directorys? The possible reason was that blastn was not correctly created

gancao commented 2 years ago

I have updated dbscan-swa.py on https://github.com/gancao/DBSCAN-SWA-1

peng-ye commented 2 years ago

that

Hi Gan Cao,

Thanks for your reply. I figured out it was indeed due to the incorrectly created blastn. I replaced the blast+ suite with another one installed by conda. Now it's working.

peng-ye commented 2 years ago

I have updated dbscan-swa.py on https://github.com/gancao/DBSCAN-SWA-1

Thanks for this update, especially the inclusion of "thread_num" in the args list. Now an updated version of that script has been proposed in the repository.