Howdy! I'm running the pipeline with a non-standar...
# taxprofilerm
Megan Justice
10/09/2025, 5:32 PMHowdy! I'm running the pipeline with a non-standard but previously published database (https://ezmeta.unige.ch/CMMG/) and trying to do bracken as well. I have run_bracken in my command and it is registering but the actual bracken command isn't running. I downloaded all the files in Krakendb/ and taxonomy/. What else do I need to do to get Bracken to actually run?
j
James Fellows Yates
10/09/2025, 8:20 PMWhat does your database.csv look like?
m
Megan Justice
10/09/2025, 8:21 PMtool,db_name,db_params,db_path
kraken2,db1,--threads 6 --classified-out classified#.fastq --unclassified-out unclassified#.fastq --paired --gzip-compressed ,/scratch/mjustice/k2_standard_20250714.tar.gz
bracken,db1,;--threads 6,/scratch/mjustice/k2_standard_20250714.tar.gz
Megan Justice
10/09/2025, 8:21 PMThose are the full contents. It actually kicked off on my last try but exceeded memory limits so I'm going to attempt to increase the memory and try again
Megan Justice
10/14/2025, 3:32 PMHey, James! I ran the pipeline with bracken and I can see some related files in the kraken2 folder (sample.bracken.kraken2.report.txt). However, the pipeline skips the other bracken steps saying it can't find the .tsv file needed. No bracken folder is made in the results section. Have you ever seen this before?
Megan Justice
10/15/2025, 1:24 AMUpdate - I had just left out the -r parameter. Added it and got the pipeline to finish with the Standard kraken2 db. Now trying to get the cmmg database run to work with bracken. It was having issues finding the files so I've kicked off a whole new instance of the pipeline to see if that fixes it.
j
James Fellows Yates
10/15/2025, 9:31 AMI would need to see the full error messages to see
James Fellows Yates
10/15/2025, 9:32 AMDoes your cmmg database have the addition
kmerm
Megan Justice
10/15/2025, 5:47 PMAhh. Ok. It does have several, but my read length is 300 and there is no 300mers file.
Megan Justice
10/15/2025, 5:49 PMI'll do some digging to find the right bracken-build command to put that together, but if you have it off hand that'd be helpful!
Megan Justice
10/15/2025, 7:50 PMI ended up just running it with the 250mer file!
j
James Fellows Yates
10/16/2025, 6:22 AMToo late, but I have a whole pipeline for building databases 😬 #C062H82UCRG (although there is a sticky bug atm with it :/)
James Fellows Yates
10/16/2025, 6:22 AMAnd 250 seems about right, you want your kmers to be shorter than your reads as a rough rule anyway