bonsai-team matam issues

bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics

GNU Affero General Public License v3.0

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issues

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Input fastq file

#120 CaroB-M opened 8 months ago
0
Specify the --cpu 4 but only 1 cpu was utilized

#118 zuopengl opened 10 months ago
0
Failed to save the components to fastq files

#117 zuopengl closed 10 months ago
0
Use Minimap2 for scaffolding instead of SortMeRNA

#116 ppericard opened 1 year ago
0
Add Changelog following current standards

#115 ppericard opened 1 year ago
0
Repatriate ComponentSearch in MATAM repo

#114 ppericard opened 1 year ago
0
Makes all read counting dependent on args.verbose

#112 tazend closed 1 year ago
4
moves all stat gathering into the if args.verbose block

#111 tazend closed 1 year ago
3
core-sga files

#110 joao1980 opened 1 year ago
0
can you please help me solve this issue

#109 triplem90manas opened 1 year ago
0
Get single marker gene from read

#108 Lcornet opened 2 years ago
0
matam_db_preprocessing.py clustering

#107 mdsufz opened 2 years ago
0
How to improve final alignement

#106 MonicaSteffi opened 2 years ago
0
Error in get the default SSU rRNA reference database

#105 duu-123 opened 2 years ago
0
Output files clarification

#104 NataliHB opened 2 years ago
0
fastq format foward only or interleaved fastq?

#103 jianshu93 opened 3 years ago
1
Questions on output file

#102 nduan1 closed 3 years ago
0
Run ktUpdateTaxonomy.sh after installing matam conda environment ?

#101 ppericard closed 4 years ago
2
SortMeRNA version needs to be fixed in MATAM conda recipe

#100 ppericard closed 4 years ago
1
Input read fastq

#99 rprops closed 4 years ago
2
matam_assembly.py crashes at ovgraphbuild stage 'non-zero return code: 136'

#98 tpriest0 closed 4 years ago
6
Reduce memory usage of scaffolding step - Limit size of SAM file from aligning contigs against complete ref db

#97 ppericard opened 4 years ago
0
Memory Error

#96 TakacsBertalan closed 4 years ago
5
Our bioconda recipe does not use the build.py script

#95 loic-couderc opened 4 years ago
1
Better error message when the input file does not exist

#94 loic-couderc opened 4 years ago
1
MATAM must not support FASTA file as input

#93 loic-couderc closed 4 years ago
0
The SystemExit exception is not enough to exit the pool worker process

#92 loic-couderc closed 4 years ago
1
Check properly the return code of system calls for sub-scripts

#91 loic-couderc closed 4 years ago
2
Add warning in README about paired reads with same exact name

#90 ppericard closed 4 years ago
0
MATAM/SGA expects Phred+33 encoded fastq files

#89 ppericard closed 4 years ago
0
Read alignment SAM file is not sorted correctly prior to score filtering

#88 ppericard opened 4 years ago
0
Replace SortMeRNA by Minimap2 for contig mapping onto the complete ref database

#87 ppericard opened 4 years ago
0
Allow compiling with newer gcc versions (up to gcc 9.1)

#86 ppericard closed 4 years ago
0
MATAM on conda uses biocore/sortmerna instead of ppericard/sortmerna which makes it slower

#85 ppericard opened 4 years ago
3
Missing classifier should not prevent matam_assembly.py from running

#84 ppericard closed 4 years ago
2
Binaries checks should be after option parsing and help printing

#83 ppericard closed 4 years ago
1
SGA binary check is missing at matam_assembly.py startup

#82 ppericard closed 4 years ago
0
Components multiprocessed assembly stalls if sga binary is not found

#81 ppericard closed 4 years ago
1
How to use paired-end data?

#80 YiweiNiu closed 4 years ago
4
Fix typo `os.basename` to `os.path.basename`

#79 kbseah closed 5 years ago
1
Add GitHub Pages for the project

#78 ppericard opened 5 years ago
0
Matam assembly error

#77 mkarlik93 closed 4 years ago
4
Add filter for very low support scaffolds (count < 1)

#76 ppericard opened 5 years ago
0
How to interpret the count= in the final assembly

#75 fanhuan closed 5 years ago
2
site hosting the matam standard DB can't be reached

#74 slambrechts closed 5 years ago
3
No option --perform_taxonomic_assignment

#73 ciemanek opened 5 years ago
4
CRITICAL - unrecognized arguments: --cup

#72 fanhuan closed 5 years ago
3
Run MATAM with large dataset

#71 yxxue closed 5 years ago
2
Homogenize database option usage (-d) when creating and using a MATAM db

#70 ppericard opened 5 years ago
0
Last version 1.5.3 on Conda

#69 lecorguille closed 5 years ago
2