Heyy you all!
I'm trying the recent q2-shotgun library for trying to find Fungal sequences in ur Shallow Shotgun Sequencing data.
Following @Micro_Biologist tutorial (Importing Kraken2 and bracken databases into qiime2!), I downloaded the PlusPF database (since this one includes fungi information) and import it to qiime2-shotgun distribution.
Then I runned kraken2 (following the github tutorial q2-books/q2-shotgun/q2-shotgun/00-tutorial.md at main · caporaso-lab/q2-books · GitHub ), apparently being this execution successful. However, when I try to run the bracken step, the following error appears:
Plugin error from moshpit:
An error was encountered while running Bracken, (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-cs94efi4.log
Taking a look at the .log file, I see that there's something wrong with the Kraken2 step, since no reads were found:
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: bracken -d /tmp/qiime2/mgorostidi/data/ab5f1fa9-9c39-4a7d-b7b4-81fd3f428998/data -i /tmp/qiime2/mgorostidi/data/24e0eb23-b553-4272-b706-d2e8d265b722/data/11326-Q-76401-0059-2019-03-08-290.report.txt -o /tmp/tmpiwgpufzu/11326-Q-76401-0059-2019-03-08-290.bracken.output.txt -w /tmp/q2-Kraken2ReportDirectoryFormat-le_95_e2/11326-Q-76401-0059-2019-03-08-290.report.txt -t 0 -r 100 -l S
Checking for Valid Options...
python src/est_abundance.py -i /tmp/qiime2/mgorostidi/data/24e0eb23-b553-4272-b706-d2e8d265b722/data/11326-Q-76401-0059-2019-03-08-290.report.txt -o /tmp/tmpiwgpufzu/11326-Q-76401-0059-2019-03-08-290.bracken.output.txt -k /tmp/qiime2/mgorostidi/data/ab5f1fa9-9c39-4a7d-b7b4-81fd3f428998/data/database100mers.kmer_distrib -l S -t 0
Checking report file: /tmp/qiime2/mgorostidi/data/24e0eb23-b553-4272-b706-d2e8d265b722/data/11326-Q-76401-0059-2019-03-08-290.report.txt
Error: no reads found. Please check your Kraken report
Could someone help me with this? Since I've checked the github issues and also the qiime2-forum but haven't found anything regarding this.
And more questions..
- This part is not included in the tutorial, but should we remove adapters from the files? (I guess yes..)
- What's the depth required for this kind of analysis?
- Having the following reads count per sample would be enough for fungal kingdom analysis?
- What's the difference between using the whole PlusPF db or the 16GB one?
- Shallow Shotgun Sequencing
- Sequences' quality graphs show good qualities
- Paired-end sequencing (each 150 length)
- demux. qzv:
THANK YOU SO MUCH IN ADVANCED