mrmckain Fast-Plast issues

mrmckain / Fast-Plast

Automated de novo assembly of whole chloroplast genomes.

MIT License

43 stars 14 forks source link

issues

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Fast plast fails with user defined bowtie2 indices

#63 Homap opened 3 months ago
0
Path

#62 ysy12306 opened 5 months ago
0
unknown issue with spades

#61 Jorge-82 opened 9 months ago
1
Update README.md

#60 mrmckain closed 10 months ago
0
problem ncbi plugin

#59 Jorge-82 opened 11 months ago
5
no result found.

#58 karthickbrlab opened 11 months ago
12
Software test data / The final result is not available.

#57 zhu416 opened 1 year ago
0
Begin Extensions / Fuse contigs loop

#56 kroeve opened 1 year ago
4
python issues

#55 Jorge-82 opened 1 year ago
1
Hit scaffolding error

#54 DenisGoryunov opened 1 year ago
3
Trimmomatic problem

#53 Jorge-82 opened 1 year ago
5
Issues with path to blast executable?

#52 ethan-baldwin opened 3 years ago
4
.fsa file empty in 5_Plastome_Finishing

#51 kmmahan opened 3 years ago
1
bowtie index not present

#50 kmmahan opened 3 years ago
3
Too many erroneous kmers

#49 kmmahan opened 3 years ago
1
No Final_Assembly result

#48 Dementieva521 opened 3 years ago
6
Suggestion to Improve Assembly

#47 nsmt89 closed 3 years ago
5
Fast-Plast finished with only two directories (1_Trimmed_Reads and 2_Bowtie_Mapping)

#46 MdkYTky closed 3 years ago
10
Issues about bowtie2

#45 jeniferclopes closed 4 years ago
3
Fast plast unable to orientate the plastome

#44 o-william-white closed 4 years ago
6
Issue with sequence_based_ir_id.pl result

#43 nsmt89 opened 4 years ago
6
Utilizing --user_bowtie

#42 nsmt89 closed 4 years ago
1
Failing SPAdes

#41 nsmt89 closed 4 years ago
3
No trimmed read files were identified to run SPAdes

#40 ef391 opened 4 years ago
6
Spades failed

#39 jhcaddisfly opened 4 years ago
1
FAILED (exit code 255)

#38 matiaskohler opened 4 years ago
1
No trimmed read files were identified to run SPAdes

#37 Angele97 opened 4 years ago
1
Final Assembly not complete

#36 NeMeh21 opened 5 years ago
7
Using user_bowtie

#35 nsmt89 closed 4 years ago
1
Afin installation

#34 carol-siniscalchi closed 4 years ago
2
Minor comments on the installation instructions

#33 nterhoeven opened 5 years ago
1
issue with bowtie completing

#32 angelajmcd closed 5 years ago
4
Directory issues

#31 mariamariamaria123 closed 4 years ago
1
file chloroplast_gene_composition_of_afin_contigs.txt is 0 bytes

#30 sagrikachugh closed 4 years ago
2
Download issues

#29 tobiasgress closed 5 years ago
0
hang in Afin stage

#28 fayweili closed 4 years ago
1
Issue with option only_coverage

#27 michaelgruenstaeudl closed 4 years ago
2
Allow for user-specified minimum region length

#26 molecules closed 5 years ago
0
Added R to list of dependencies

#25 molecules closed 5 years ago
0
Fix construction of some file names

#24 molecules closed 6 years ago
0
Make fast-plast.pl executable

#23 molecules closed 6 years ago
0
Question: orientation of the chloroplast regions

#22 PfaffS closed 6 years ago
2
Add Bangiales chloroplast genomes to data set

#21 kmendler closed 6 years ago
2
Global symbol "$TRIMMOMATIC" requires explicit package name

#20 scrameri closed 6 years ago
2
Difficulty in running in shared environment

#19 molecules closed 6 years ago
4
Clarify that Perl 5.x with threading is needed

#18 molecules closed 6 years ago
0
Patching fast-plast.pl to handle multistream compressed gzip files

#17 molecules closed 6 years ago
2
Error with "--skip trim"

#16 dfmoralesb closed 4 years ago
8
tempbow variable declaration

#15 zapatalab closed 6 years ago
2
Check input files exist

#14 dwjp closed 6 years ago
1