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metageni / SUPER-FOCUS

A tool for agile functional analysis of shotgun metagenomic data
GNU General Public License v3.0
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rapsearch database cannot open #50

Closed s4251484 closed 5 years ago

s4251484 commented 5 years ago

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!

Screen Shot 2019-04-13 at 6 24 00 pm

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.

Screen Shot 2019-04-13 at 6 41 38 pm
s4251484 commented 5 years ago

Sorry @metageni please close this issue. turn out that the info file was renamed, hence the script couldnt work.

metageni commented 5 years ago

@s4251484 No problem. prerapsearch is the tool to format the database and rapsearch is the aligner - that is why the confusion.