khyox/recentrifuge issues and pull requests

#54 - Add threads options, why and how

Issue - State: open - Opened by jfouret about 2 months ago - 2 comments
Labels: enhancement

#53 - Error code 13?

Issue - State: closed - Opened by BZed81 6 months ago - 1 comment
Labels: invalid

#52 - taxonomy files for common 16S datasets?

Issue - State: open - Opened by faylward 8 months ago
Labels: help wanted, question

#51 - Building nt database - no multithreading at centrifuge-build step

Issue - State: closed - Opened by koppk 10 months ago - 5 comments
Labels: help wanted, centrifuge

#50 - OverflowError when trying passing centrifuge input test

Issue - State: closed - Opened by pimarin 10 months ago - 3 comments

#49 - ImportError: cannot import name 'SequentialSequenceWriter' from 'Bio.SeqIO.Interfaces'

Issue - State: closed - Opened by pimarin over 1 year ago - 9 comments
Labels: bug, biopython

#48 - Issue with nodes/names missing unclassified readID (0)

Issue - State: closed - Opened by Electrocyte over 1 year ago - 1 comment
Labels: ncbi

#47 - float deprecated in numpy 1.24

Issue - State: closed - Opened by Electrocyte over 1 year ago - 1 comment

#46 - Rextract from Kraken2 output

Issue - State: closed - Opened by buiguesj about 2 years ago - 1 comment
Labels: question

#45 - refasplit output files with non-padded zeros

Issue - State: closed - Opened by khyox over 2 years ago
Labels: bug, refasplit

#44 - Score understanding

Issue - State: closed - Opened by lvelosuarez over 2 years ago - 1 comment
Labels: question

#43 - (question) produced output

Issue - State: closed - Opened by arz19893 over 2 years ago - 1 comment
Labels: help wanted, question, kraken

#42 - Enhancement: provide control samples in a different directory

Issue - State: open - Opened by khyox over 2 years ago
Labels: enhancement

#41 - abundance table as output

Issue - State: closed - Opened by rjsorr over 2 years ago - 1 comment
Labels: question

#40 - interpreting log file for contamination removal

Issue - State: open - Opened by rjsorr over 2 years ago - 3 comments
Labels: enhancement, help wanted, question

#39 - definition of contaminat level for removal?

Issue - State: closed - Opened by rjsorr over 2 years ago - 1 comment
Labels: help wanted, question

#38 - Contamination removal help and too large HTML files

Issue - State: open - Opened by rjsorr over 2 years ago - 11 comments
Labels: enhancement, help wanted, kraken

#37 - -k for multiple directories of .krk files?

Issue - State: closed - Opened by rjsorr over 2 years ago - 3 comments
Labels: enhancement, question, kraken

#36 - rextract: ZeroDivisionError

Issue - State: closed - Opened by shrivastavabhishek over 2 years ago - 3 comments
Labels: enhancement, rextract

#35 - Compatibility with Ganon?

Issue - State: closed - Opened by rjsorr over 2 years ago - 5 comments
Labels: help wanted, question

#34 - ZeroDivisionError

Issue - State: closed - Opened by jagos01 over 3 years ago - 2 comments
Labels: help wanted, centrifuge

#33 - Data from article "Recentrifuge: Robust comparative analysis and contamination removal for metagenomics"

Issue - State: closed - Opened by kla44 over 3 years ago - 2 comments
Labels: help wanted, question

#32 - unclassified reads in rextract

Issue - State: closed - Opened by comixwang over 3 years ago - 1 comment
Labels: duplicate, enhancement, rextract

#31 - parameter -y/--minscore in rextract

Issue - State: closed - Opened by fancyge over 3 years ago - 10 comments
Labels: help wanted, question, rextract

#30 - rextract: zipped fastq files

Issue - State: closed - Opened by fancyge over 3 years ago - 7 comments
Labels: enhancement, help wanted

#29 - min() arg is an empty sequence [error]

Issue - State: closed - Opened by JChristopherEllis almost 4 years ago - 4 comments
Labels: kraken

#28 - rextract: add option to get the unclassified reads

Issue - State: closed - Opened by khyox almost 4 years ago
Labels: enhancement, centrifuge, rextract

#27 - rextract: read retrieval failed

Issue - State: closed - Opened by webbchen almost 4 years ago - 8 comments
Labels: centrifuge, biopython

#26 - More than 10 mins on a centrifuge result (21.3 MB)

Issue - State: closed - Opened by yeli7068 almost 4 years ago - 1 comment
Labels: help wanted

#25 - The instructions for installing are extremely unclear

Issue - State: closed - Opened by zmunro about 4 years ago - 1 comment
Labels: help wanted

#24 - Bug Report: PermissionError: [Errno 13] Permission denied

Issue - State: closed - Opened by hansir8 over 4 years ago - 3 comments
Labels: help wanted

#23 - KeyError: 'STRAIN'

Issue - State: closed - Opened by abomba over 4 years ago - 5 comments
Labels: bug, ncbi

#22 - ZeroDivisionError/Centrifuge

Issue - State: closed - Opened by ganiatgithub over 4 years ago - 3 comments
Labels: help wanted, centrifuge

#21 - Update kraken.py to support compressed inputs

Pull Request - State: closed - Opened by XiaoJianfeng over 4 years ago - 1 comment
Labels: enhancement, kraken

#20 - update kraken.py to support compressed input

Pull Request - State: closed - Opened by XiaoJianfeng over 4 years ago

#19 - Can command "rextract" support to extract reads from fasta files?

Issue - State: closed - Opened by hansir8 almost 5 years ago - 3 comments
Labels: enhancement

#18 - divided by zero error - fault by using krakenuniq?

Issue - State: closed - Opened by BioNij about 5 years ago - 3 comments

#17 - The last stable release of pandas is breaking retest

Issue - State: closed - Opened by khyox over 5 years ago
Labels: bug, pandas

#16 - retest error: "remock: error: one of the arguments -m/--mock is required"

Issue - State: closed - Opened by lkmklsmn over 5 years ago - 2 comments

#15 - recentrifuge.rank.UnsupportedTaxLevelError: Unknown tax level section

Issue - State: closed - Opened by oatesa over 5 years ago - 3 comments

#14 - Krona generation fails: all seqs are orphans?

Issue - State: closed - Opened by wolfgangrumpf over 5 years ago - 6 comments
Labels: enhancement, kraken

#13 - No sequence passed the filter error

Issue - State: closed - Opened by mhyleung over 5 years ago - 6 comments
Labels: kraken

#12 - Using centrifuge premade (.cf) database

Issue - State: closed - Opened by benkraj over 5 years ago - 5 comments
Labels: help wanted, question, ncbi

#11 - retest fails on MacOS

Issue - State: closed - Opened by BenKaehler almost 6 years ago - 5 comments
Labels: bug, matplotlib, conda

#10 - Recentrifuge fails because of new NCBI taxonomy rank: subcohort

Issue - State: closed - Opened by khyox almost 6 years ago - 1 comment
Labels: bug, ncbi

#9 - CSV output

Issue - State: closed - Opened by my-serendipity about 6 years ago - 3 comments
Labels: enhancement

#8 - Excel output with empty columns

Issue - State: closed - Opened by blwe about 6 years ago - 6 comments
Labels: bug

#7 - Test files?

Issue - State: closed - Opened by sminot about 6 years ago - 2 comments

#6 - export PDF from recentrifuge results?

Issue - State: closed - Opened by HanZhenZ about 6 years ago - 2 comments
Labels: help wanted, question

GitHub / khyox/recentrifuge issues and pull requests