vrmarcelino/CCMetagen issues and pull requests

#67 - No such file or directory error

Issue - State: open - Opened by jeremysutherland about 2 months ago - 3 comments

#66 - error "out of memory"

Issue - State: open - Opened by tulikasriv26 6 months ago - 7 comments

#65 - Merge branch `dev` into `master` - `v1.5.0`

Pull Request - State: closed - Opened by vinisalazar 6 months ago

#64 - Restore master branch

Pull Request - State: closed - Opened by vinisalazar 6 months ago

#63 - Database headers

Issue - State: closed - Opened by vinisalazar 7 months ago - 4 comments

#62 - Tests

Pull Request - State: closed - Opened by vinisalazar 7 months ago

#61 - error in taxdump.tar.gz

Issue - State: closed - Opened by igsbma 8 months ago - 4 comments

#60 - Prebuilt indexes unavailable

Issue - State: open - Opened by MortenEneberg 10 months ago - 10 comments

#59 - Code improvements

Pull Request - State: closed - Opened by vinisalazar 10 months ago

#58 - Tidy up repository

Pull Request - State: closed - Opened by vinisalazar 10 months ago

#57 - Update setup

Pull Request - State: closed - Opened by vinisalazar 10 months ago

#56 - CCMetagen `1.4.2` - test release

Pull Request - State: closed - Opened by vinisalazar 10 months ago - 1 comment

#55 - IndexError: list index out of range

Issue - State: closed - Opened by pedres 10 months ago - 4 comments

#54 - How much memory does kma require?

Issue - State: closed - Opened by hehanhhh about 1 year ago - 3 comments

#53 - ValueError for taxid when using custom database

Issue - State: closed - Opened by brambloemen about 1 year ago - 2 comments

#52 - /bin/sh: 1: ktImportText: Permission denied

Issue - State: closed - Opened by lichen-fungus about 1 year ago - 3 comments

#51 - Indexing custom database returns empty *.length.b file

Issue - State: closed - Opened by longwayl about 1 year ago - 1 comment

#50 - download the "ncbi_nt_no_env_11jun2019" database error

Issue - State: closed - Opened by hehanhhh over 1 year ago - 5 comments

#49 - Unexpected end of file and Malformed input error

Issue - State: closed - Opened by Rohit-Satyam over 1 year ago - 2 comments

#48 - TypeError: 'NoneType' object is not iterable

Issue - State: closed - Opened by fernanarr over 1 year ago - 7 comments

#47 - Total reads equal to twice the number of fragments?

Issue - State: closed - Opened by alvanuffelen over 1 year ago - 9 comments

#46 - 310 Segmentation fault (core dumped)

Issue - State: closed - Opened by taniagmangolini over 1 year ago - 2 comments

#45 - Found very few number of fungi

Issue - State: closed - Opened by DrYoungOG almost 2 years ago - 1 comment

#44 - Discrepancy on the number of fragments between ccm.csv and kmaout.frag.

Issue - State: closed - Opened by anacarolsoares almost 2 years ago - 5 comments

#43 - Error with CCMetagen.py

Issue - State: closed - Opened by DrYoungOG almost 2 years ago - 3 comments

#42 - Something Error of KMA

Issue - State: closed - Opened by TaoCheng98 almost 2 years ago - 7 comments

#41 - Segmentation error in KMA

Issue - State: closed - Opened by taniagmangolini about 2 years ago - 3 comments

#40 - When using a custom DB, metagen.py -r nt doesn't recognise any NCBI taxa

Issue - State: closed - Opened by Steven-Kemp over 2 years ago - 2 comments

#39 - New reference databases

Issue - State: closed - Opened by yashasdevasurmutt over 2 years ago - 1 comment

#38 - Unable to unzip the downloaded database

Issue - State: closed - Opened by Rohit-Satyam over 2 years ago - 11 comments

#37 - Read error in KMA Mapping

Issue - State: closed - Opened by tuck82er over 2 years ago - 5 comments

#36 - Unable to construct database following your instruction

Issue - State: closed - Opened by liuchen92 over 2 years ago - 3 comments

#35 - Index out of range when using CCMetagen.py

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

#34 - ValueError: 1327640 taxid not found

Issue - State: closed - Opened by taniagmangolini over 2 years ago - 3 comments

#33 - Database download problem

Issue - State: closed - Opened by AMPByrne almost 3 years ago - 1 comment

#32 - kma error 2

Issue - State: closed - Opened by vasudhajain29 almost 3 years ago - 9 comments

#31 - parameters for low-biomass samples

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

#30 - ValueError: invalid literal for int() with base 10: 'NW_001849834.1

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

#29 - Changed populate_w_tax function

Pull Request - State: closed - Opened by karentherkelsen over 3 years ago

#28 - Added Krona plot mode option

Pull Request - State: closed - Opened by karentherkelsen over 3 years ago

#27 - Issue installing libz-dev

Issue - State: closed - Opened by qfaber over 3 years ago - 1 comment

#26 - how to represent top most abundant species

Issue - State: closed - Opened by saras224 over 3 years ago - 2 comments

#25 - CCMetagen_merge input suffix discrepancy

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

#24 - rename_nt.py is not considering multi seq IDs in fasta headers

Issue - State: closed - Opened by mihkelvaher over 3 years ago - 1 comment

#23 - Underestimation possibility of abundance while using db containing subsequences?

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

#22 - Databases-related inquiry

Issue - State: closed - Opened by Ahmed-Shibl almost 4 years ago - 5 comments

#21 - Obtaining RPM, fragments, and proportion of mapper reads

Issue - State: closed - Opened by Tj-Idowu almost 4 years ago - 2 comments

#20 - Machine specs for making a large custom database

Issue - State: closed - Opened by akramirez almost 4 years ago - 6 comments

#19 - Run out of memory

Issue - State: closed - Opened by SethCommichaux almost 4 years ago - 2 comments

#18 - Custom Database

Issue - State: closed - Opened by punnettsun about 4 years ago - 3 comments

#17 - multiple lanes (paired end) for each sample

Issue - State: closed - Opened by molbio7 about 4 years ago - 1 comment

#16 - Abundance Calculation

Issue - State: closed - Opened by punnettsun about 4 years ago - 4 comments

#15 - Classified/Unclassified Reads

Issue - State: closed - Opened by punnettsun about 4 years ago - 2 comments

#14 - CCMetagen.py: mysql error when setting up the taxonomy database

Issue - State: closed - Opened by walshaw about 4 years ago - 5 comments

#13 - CCMetagen_merge.py output columns meaning

Issue - State: closed - Opened by theo-allnutt-bioinformatics about 4 years ago - 1 comment

#12 - suggestion: merge species but not files

Issue - State: closed - Opened by theo-allnutt-bioinformatics about 4 years ago - 4 comments

#11 - Depth unit question

Issue - State: closed - Opened by theo-allnutt-bioinformatics about 4 years ago - 2 comments

#10 - pandas error

Issue - State: closed - Opened by theo-allnutt-bioinformatics about 4 years ago - 6 comments

#9 - acc2taxid.map

Issue - State: closed - Opened by theo-allnutt-bioinformatics about 4 years ago - 2 comments

#8 - Feature request: unmapped/unknown contigs

Issue - State: closed - Opened by cabbagesofdoom over 4 years ago - 5 comments

GitHub / vrmarcelino/CCMetagen issues and pull requests