rapsearch database cannot open
s4251484 opened this issue · comments
Hi @metageni i'm receiving this error when i try running superfocus with rapsearch database, but it runs perfectly when i run it with diamond! strange~
Queries are nucleotide sequences in fasta format
Can not open the database file
Please check the file name
Main END
Time used: 0 min (0.0 hours)
[2019-04-13 18:12:43,801 - INFO] Parsing Alignments
Traceback (most recent call last):
File "/gpfs1/scratch/30days/s4251484/condaenv/qctrim/bin/superfocus", line 11, in
load_entry_point('superfocus==0.0.0', 'console_scripts', 'superfocus')()
File "/gpfs1/scratch/30days/s4251484/condaenv/qctrim/lib/python3.7/site-packages/superfocus_app/superfocus.py", line 342, in main
del_alignments)
ValueError: not enough values to unpack (expected 2, got 0)
i'm wondering is it because of this difference (see attachment) between rapsearch and diamond in the downloadDB.py? where "format(dbname, WORK_DIRECTORY, dbname)" are at different row???
appreciate your help! thank you!
These are the files in my lib/python3.7/site-packages/superfocus_app/db/static/rapsearch2 folder - please let me know if they are named incorrectly. thank you.
Sorry @metageni please close this issue. turn out that the info file was renamed, hence the script couldnt work.
@s4251484 No problem. prerapsearch is the tool to format the database and rapsearch is the aligner - that is why the confusion.