Comments (3)
Thanks for the report, Erik. Recentrifuge is not currently supporting Krakenuniq. I have no personal experience with that classifier, but if you can direct it to generate its output files in the typical Kraken format, you could use rcf
to parse the files straightforwardly. Another solution could be to use Recentrifuge's generic parser with your (already generated) Krakenuniq files. Please see running Recentrifuge for a generic classifier for more details. If you need further help with this, feel free to send me (or copypaste here) the head and some representative lines of your output files so that I could figure it out.
from recentrifuge.
Hi,
Thanks for the suggestion, and this is with regard to the issue I posted on centrifuge DaehwanKimLab/centrifuge#190
My command of running rextract is:
conda activate recentrifuge rextract -f centrifuge-hvc.txt -i 694009 -q Run02_filtered.fastq -n ~/miniconda/envs/recentrifuge/bin/taxdump/
I got the same zero division error:
Traceback (most recent call last): File "/home/Staff/uqgni1/miniconda2/envs/recentrifuge/bin/rextract", line 347, in <module> main() File "/home/Staff/uqgni1/miniconda2/envs/recentrifuge/bin/rextract", line 241, in main print(f' \033[90mMatching reads: \033[0m{len(records):_d} \033[90m\t' ZeroDivisionError: division by zero
When I do head
on my centrifuge output, it looks like:
name taxID taxRank genomeSize numReads numUniqueReads abundance
Homo sapiens 9606 species 3272089205 11164 8884 0.0
Human alphaherpesvirus 2 10310 species 154675 1 1 0.0
Cercopithecine alphaherpesvirus 2 10317 species 150715 1 0 0.0
Bovine alphaherpesvirus 1 10320 species 135301 8 0 0.0
This should be fine, right?
Any tips on troubleshooting?
from recentrifuge.
Hi @ganiatgithub,
Please open a new issue so that you fill all the required data that will help me to troubleshoot this issue.
In addition, the output of centrifuge that you show is different from what Recentrifuge expects so, please, when you open the new issue, please add also the complete line of the Centrifuge command that you used to get such centrifuge output.
Thank you!
from recentrifuge.
Related Issues (20)
- ZeroDivisionError HOT 2
- Compatibility with Ganon? HOT 5
- rextract: ZeroDivisionError HOT 3
- -k for multiple directories of .krk files? HOT 3
- Contamination removal help and too large HTML files HOT 11
- definition of contaminat level for removal? HOT 1
- interpreting log file for contamination removal HOT 3
- abundance table as output HOT 1
- Enhancement: provide control samples in a different directory
- (question) produced output HOT 1
- Score understanding HOT 1
- refasplit output files with non-padded zeros
- Rextract from Kraken2 output HOT 1
- float deprecated in numpy 1.24 HOT 1
- Issue with nodes/names missing unclassified readID (0) HOT 1
- ImportError: cannot import name 'SequentialSequenceWriter' from 'Bio.SeqIO.Interfaces' HOT 9
- OverflowError when trying passing centrifuge input test HOT 3
- Building nt database - no multithreading at centrifuge-build step HOT 5
- taxonomy files for common 16S datasets?
- Error code 13? HOT 1
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from recentrifuge.