flass pantagruel issues

flass / pantagruel

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome

GNU General Public License v3.0

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issues

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in -u mode, make the numbering of homogeneous gene families (coding identical proteins) consistent with source db

#50 flass opened 1 year ago
0
Error while installing dependencies

#49 jhcuarta closed 2 years ago
2
Could not dowload interproscan 1 computed checksum did NOT match

#48 jhcuarta closed 2 years ago
1
Permission denied to delete assembly files after failed fetch

#47 ezherman closed 2 years ago
4
Task 04 failed: InterProScan version check

#46 mattbawn closed 3 years ago
1
ERROR: step 6: failed comparing each clade-specific core genome

#45 MartinezRuiz-Carlos opened 3 years ago
28
TASK 5 Failed: failed search of populations in reference tree

#44 mattbawn closed 3 years ago
1
No internet connection and speclist

#43 mattbawn closed 3 years ago
1
Step 08 clade_specific_genes: ERROR: step 5.1: failed

#42 MartinezRuiz-Carlos closed 3 years ago
6
extracting metadata from GenBank dictionary error

#41 mattbawn closed 3 years ago
9
finish GeneRax parser / interface for tasks 08 and 09

#40 flass opened 3 years ago
0
Step 7 (reconciliation) ending with no output?

#39 MartinezRuiz-Carlos closed 3 years ago
13
MrBayes (step 06) extremely slow?

#38 MartinezRuiz-Carlos closed 4 years ago
1
task 7 inconstitency

#37 kuzman1306 closed 4 years ago
1
Task 6: HPC scripts

#36 megaptera-helvetiae closed 4 years ago
13
HPC scripts now documented

#35 flass closed 4 years ago
0
missing igraph

#34 megaptera-helvetiae closed 4 years ago
1
InterproScan was not found on this machine: cannot run this (facultative) task of Pantagruel pipeline; exit now

#33 mattbawn closed 4 years ago
3
Task 5 failed: How to install lsd on server

#32 megaptera-helvetiae closed 4 years ago
1
ERROR: Pantagruel pipeline task 1: failed.

#31 mattbawn closed 4 years ago
2
Task 4: InterproScan was not found on this machine

#30 megaptera-helvetiae closed 4 years ago
5
ERROR: something went wrong when modifying the GenBank flat file

#29 mattbawn closed 4 years ago
5
task 3: create sqldb: KeyError: 'locus_tag_prefix'

#28 megaptera-helvetiae closed 4 years ago
3
Cannot access .../*.gbk files after running prokka for custom genomes

#27 megaptera-helvetiae closed 4 years ago
12
Updating the software when working on a server without administrator rights

#26 megaptera-helvetiae closed 4 years ago
1
Pantagrel pipeline task 0: failed, adding region features to GFF file

#25 mattbawn closed 4 years ago
12
NCBI manually download genomes

#24 mattbawn closed 4 years ago
3
Error: init failed

#23 mattbawn closed 4 years ago
3
Alternative to mget and lfpt

#22 sarah872 closed 4 years ago
1
ls: cannot access spades_contigs_db/spades_contigs_db/00.input_data/annotation/J16_strain.contigs/*.gbk: No such file or directory

#21 sarah872 closed 4 years ago
5
pantagruel_pipeline_00_fetch_data.sh

#20 samlipworth closed 4 years ago
2
Pantagrel pipeline task 5: failed

#19 kuzman1306 closed 4 years ago
7
Task 0 failed

#18 Sebastien-Raguideau closed 4 years ago
4
task 3: speclist download

#17 kuzman1306 closed 4 years ago
1
task 0 failed

#16 kuzman1306 closed 4 years ago
6
Wrong test for lsd in dependency install

#15 pveber closed 5 years ago
1
init: failed

#14 kuzman1306 closed 5 years ago
3
Task 0 failed : Cannot assign requested address

#13 Sebastien-Raguideau closed 4 years ago
5
Task 5 failed; Tasks 0,1,2,3 were completed but their output files do not look complete.

#12 kihyunee closed 4 years ago
20
Dockerfile

#11 pveber closed 4 years ago
7
[suggestion] provide installation formulas

#10 sam217pa closed 5 years ago
1
some commands missing

#9 ElitaJaun closed 5 years ago
3
Add option to directly query NCBI Assembly database

#8 flass opened 5 years ago
0
Usage: task 5 error

#7 ElitaJaun closed 5 years ago
3
added a minimal test dataset

#6 flass closed 5 years ago
0
Usage: errors when using pantagruel command with TASKS

#5 ElitaJaun closed 5 years ago
1
Usage: the init command - not working

#4 ElitaJaun closed 5 years ago
3
Java version and InterProScan

#3 ElitaJaun closed 5 years ago
3
links in generated outputs

#2 pveber closed 5 years ago
1
problems running pantagruel commands

#1 ElitaJaun closed 5 years ago
2