Open shreya1singh728 opened 1 year ago
Hii, I am running DBSCAN-SWA on a large dataset and I am facing this error on some files.
Building reference index... [0.788333s] Building query index... [0.006586s] Building seed filter... [0.042056s] Searching alignments... [0.031454s] Processing query chunk 0, reference chunk 0, shape 0, index chunk 2. Building reference index... [0.855179s] Building query index... [0.007275s] Building seed filter... [0.041847s] Searching alignments... [0.031047s] Processing query chunk 0, reference chunk 0, shape 0, index chunk 3. Building reference index... [0.743206s] Building query index... [0.006322s] Building seed filter... [0.042643s] Searching alignments... [0.029082s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 0. Building reference index... [0.729244s] Building query index... [0.006085s] Building seed filter... [0.04255s] Searching alignments... [0.029532s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 1. Building reference index... [0.76787s] Building query index... [0.006812s] Building seed filter... [0.042375s] Searching alignments... [0.028811s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 2. Building reference index... [0.802298s] Building query index... [0.006647s] Building seed filter... [0.04129s] Searching alignments... [0.02878s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 3. Building reference index... [0.745652s] Building query index... [0.006103s] Building seed filter... [0.041592s] Searching alignments... [0.027827s] Deallocating buffers... [0.027922s] Computing alignments... [2.45037s] Deallocating reference... [0.015322s] Loading reference sequences... [0.000523s] Deallocating buffers... [0.000536s] Deallocating queries... [0.000546s] Loading query sequences... [0.000432s] Closing the input file... [0.000357s] Closing the output file... [0.000669s] Closing the database file... [0.000352s] Deallocating taxonomy... [0.000322s] Total time = 37.9623s Reported 15082 pairwise alignments, 15123 HSPs. 815 queries aligned. start to visualize the results! Traceback (most recent call last): File "/home/shreya/DBSCAN-SWA-1/bin/dbscan-swa.py", line 2807, in predict_prophage(strain_id,inputfile_bac,outdir,add_annotation,prefix) File "/home/shreya/DBSCAN-SWA-1/bin/dbscan-swa.py", line 2587, 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,prefix) File "/home/shreya/DBSCAN-SWA-1/bin/dbscan-swa.py", line 2138, in visualize prophage_id = line.split('\n')[0].strip().split('|')[1]
IndexError: list index out of range
Hii, I am running DBSCAN-SWA on a large dataset and I am facing this error on some files.
Building reference index... [0.788333s] Building query index... [0.006586s] Building seed filter... [0.042056s] Searching alignments... [0.031454s] Processing query chunk 0, reference chunk 0, shape 0, index chunk 2. Building reference index... [0.855179s] Building query index... [0.007275s] Building seed filter... [0.041847s] Searching alignments... [0.031047s] Processing query chunk 0, reference chunk 0, shape 0, index chunk 3. Building reference index... [0.743206s] Building query index... [0.006322s] Building seed filter... [0.042643s] Searching alignments... [0.029082s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 0. Building reference index... [0.729244s] Building query index... [0.006085s] Building seed filter... [0.04255s] Searching alignments... [0.029532s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 1. Building reference index... [0.76787s] Building query index... [0.006812s] Building seed filter... [0.042375s] Searching alignments... [0.028811s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 2. Building reference index... [0.802298s] Building query index... [0.006647s] Building seed filter... [0.04129s] Searching alignments... [0.02878s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 3. Building reference index... [0.745652s] Building query index... [0.006103s] Building seed filter... [0.041592s] Searching alignments... [0.027827s] Deallocating buffers... [0.027922s] Computing alignments... [2.45037s] Deallocating reference... [0.015322s] Loading reference sequences... [0.000523s] Deallocating buffers... [0.000536s] Deallocating queries... [0.000546s] Loading query sequences... [0.000432s] Closing the input file... [0.000357s] Closing the output file... [0.000669s] Closing the database file... [0.000352s] Deallocating taxonomy... [0.000322s] Total time = 37.9623s Reported 15082 pairwise alignments, 15123 HSPs. 815 queries aligned. start to visualize the results! Traceback (most recent call last): File "/home/shreya/DBSCAN-SWA-1/bin/dbscan-swa.py", line 2807, in
predict_prophage(strain_id,inputfile_bac,outdir,add_annotation,prefix)
File "/home/shreya/DBSCAN-SWA-1/bin/dbscan-swa.py", line 2587, 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,prefix)
File "/home/shreya/DBSCAN-SWA-1/bin/dbscan-swa.py", line 2138, in visualize
prophage_id = line.split('\n')[0].strip().split('|')[1]