search

AbateLab / SiC-seq

Scripts used in the 2017 SiC-seq paper
3 stars 3 forks source link

Error When Running kraken.py #3

Open jrede opened 4 years ago

jrede commented 4 years ago

Hi @bdemaree

I was hoping you could help me solve this error. The kraken database I used only comprises only Alteromonas genomes, and the sqlite database only contains SRR5208456. Thank you for any help!

command used:

python2 kraken.py --SE \
sicseq_456-ACE-50barCutoff.db

Error:

Creating table for Kraken data... Table kraken set up successfully. 6561396 sequences (836.53 Mbp) processed in 34.970s (11257.8 Kseq/m, 1435.28 Mbp/m). 42099 sequences classified (0.64%) 6519297 sequences unclassified (99.36%) Traceback (most recent call last): File "kraken.py", line 289, in kraken() # Run Kraken and insert data into sqlite db File "kraken.py", line 218, in kraken (tableK, domain, phylum, Class, order, family, genus, species, barcode, barID)) sqlite3.OperationalError: no such table: kraken

jrede commented 4 years ago

The issue must have been in how I made the database. I downloaded the 8 gig mini-kraken database to test and it completed, however, no reads were added to the database! This shouldn't be correct, right? Because the default setting the script is to use mini-kraken.