khyox recentrifuge issues

khyox / recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

http://www.recentrifuge.org

Other

86 stars 7 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Add threads options, why and how

#54 jfouret opened 2 months ago
2
Error code 13?

#53 BZed81 closed 6 months ago
1
taxonomy files for common 16S datasets?

#52 faylward opened 8 months ago
0
Building nt database - no multithreading at centrifuge-build step

#51 koppk closed 5 months ago
5
OverflowError when trying passing centrifuge input test

#50 pimarin closed 10 months ago
3
ImportError: cannot import name 'SequentialSequenceWriter' from 'Bio.SeqIO.Interfaces'

#49 pimarin closed 11 months ago
9
Issue with nodes/names missing unclassified readID (0)

#48 Electrocyte closed 1 year ago
1
float deprecated in numpy 1.24

#47 Electrocyte closed 1 year ago
1
Rextract from Kraken2 output

#46 buiguesj closed 11 months ago
1
refasplit output files with non-padded zeros

#45 khyox closed 2 years ago
0
Score understanding

#44 lvelosuarez closed 11 months ago
1
(question) produced output

#43 arz19893 closed 11 months ago
1
Enhancement: provide control samples in a different directory

#42 khyox opened 2 years ago
0
abundance table as output

#41 rjsorr closed 11 months ago
1
interpreting log file for contamination removal

#40 rjsorr opened 2 years ago
3
definition of contaminat level for removal?

#39 rjsorr closed 2 years ago
1
Contamination removal help and too large HTML files

#38 rjsorr opened 2 years ago
11
-k for multiple directories of .krk files?

#37 rjsorr closed 2 years ago
3
rextract: ZeroDivisionError

#36 shrivastavabhishek closed 2 years ago
3
Compatibility with Ganon?

#35 rjsorr closed 2 years ago
5
ZeroDivisionError

#34 jagos01 closed 3 years ago
2
Data from article "Recentrifuge: Robust comparative analysis and contamination removal for metagenomics"

#33 kla44 closed 3 years ago
2
unclassified reads in rextract

#32 comixwang closed 3 years ago
1
parameter -y/--minscore in rextract

#31 fancyge closed 3 years ago
10
rextract: zipped fastq files

#30 fancyge closed 3 years ago
7
min() arg is an empty sequence [error]

#29 JChristopherEllis closed 3 years ago
4
rextract: add option to get the unclassified reads

#28 khyox closed 2 years ago
0
rextract: read retrieval failed

#27 webbchen closed 3 years ago
8
More than 10 mins on a centrifuge result (21.3 MB)

#26 yeli7068 closed 4 years ago
1
The instructions for installing are extremely unclear

#25 zmunro closed 4 years ago
1
Bug Report: PermissionError: [Errno 13] Permission denied

#24 hansir8 closed 4 years ago
3
KeyError: 'STRAIN'

#23 abomba closed 4 years ago
5
ZeroDivisionError/Centrifuge

#22 ganiatgithub closed 4 years ago
3
Update kraken.py to support compressed inputs

#21 XiaoJianfeng closed 4 years ago
1
update kraken.py to support compressed input

#20 XiaoJianfeng closed 4 years ago
0
Can command "rextract" support to extract reads from fasta files?

#19 hansir8 closed 4 years ago
3
divided by zero error - fault by using krakenuniq?

#18 BioNij closed 4 years ago
3
The last stable release of pandas is breaking retest

#17 khyox closed 5 years ago
0
retest error: "remock: error: one of the arguments -m/--mock is required"

#16 lkmklsmn closed 5 years ago
2
recentrifuge.rank.UnsupportedTaxLevelError: Unknown tax level section

#15 oatesa closed 5 years ago
3
Krona generation fails: all seqs are orphans?

#14 wolfgangrumpf closed 5 years ago
6
No sequence passed the filter error

#13 mhyleung closed 3 years ago
6
Using centrifuge premade (.cf) database

#12 benkraj closed 5 years ago
5
retest fails on MacOS

#11 BenKaehler closed 5 years ago
5
Recentrifuge fails because of new NCBI taxonomy rank: subcohort

#10 khyox closed 5 years ago
1
CSV output

#9 my-serendipity closed 6 years ago
3
Excel output with empty columns

#8 blwe closed 6 years ago
6
Test files?

#7 sminot closed 6 years ago
2
export PDF from recentrifuge results?

#6 HanZhenZ closed 5 years ago
2
what the unassgined means?

#5 yeli7068 closed 6 years ago
2