jpuritz dDocent issues - Githubissues

jpuritz / dDocent

a bash pipeline for RAD sequencing

ddocent.com

MIT License

52 stars 42 forks source link

issues

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Info about the number of mapped reads etc.

#90 Anto007 closed 6 months ago
5
Jpuritz patch 1

#89 jpuritz closed 6 months ago
1
Question about ErrorCount.sh

#88 eprdz closed 6 months ago
1
#'head: cannot open 'reference.fasta' for reading: No such file or directory' while running denovo assembly

#87 santoshkumarrana closed 6 months ago
3
sh: /dev/tty: No such device or address

#86 Anto007 closed 6 months ago
1
Genomic interval creation failed

#85 tamsinlh opened 2 years ago
3
replace ls and rm with find

#84 pdimens opened 2 years ago
0
too many arguments for ls and rm

#83 pdimens opened 2 years ago
0
missing data in merged vcf file

#82 alxcmrn closed 6 months ago
1
clarify manual installation

#81 pdimens closed 2 years ago
0
popmap creation logic

#80 pdimens closed 2 years ago
0
ulimit silent error (bug)

#79 pdimens closed 6 months ago
1
remove duplicates prior to variant calling

#78 pdimens closed 3 years ago
2
fastp v 0.19.5 issue

#77 atfields closed 3 years ago
0
Suggested parameters for bam filtering

#76 atfields opened 3 years ago
5
Fixed file name missing error

#75 llalon closed 3 years ago
0
update install and runtime deps, add bedops merge

#74 pdimens closed 3 years ago
3
Spruce up readme

#73 pdimens closed 3 years ago
2
performance bottleneck

#72 pdimens closed 3 years ago
1
Very inefficent scan of full reference genome

#71 ne1s0n closed 3 years ago
2
CD-HIT runs forever / never finishes

#70 mscharmann closed 3 years ago
2
miniconda recipe with samtools bug?

#69 j-a-thia closed 3 years ago
1
Use bedops instead of bedools merge for memory efficiency

#68 ne1s0n closed 3 years ago
5
ReferenceOpt.sh - kopt.data output

#67 j-a-thia closed 4 years ago
1
please make a new release on github

#66 bernt-matthias closed 3 years ago
1
Program stuck in using BWA mapping reads

#65 Liut035 closed 3 years ago
2
Update dDocent_filters final prompt

#64 pdimens closed 4 years ago
0
Downgrade conda vcftools version dependency

#63 pdimens closed 4 years ago
2
Error with main script - EOF management

#62 ne1s0n closed 4 years ago
1
Update RefMapOpt.sh

#61 TomaszSuchan closed 4 years ago
1
RefMapOpt error

#60 TomaszSuchan closed 4 years ago
1
Fastp not getting number of processors

#59 kubu4 closed 4 years ago
3
Simple Suggestions To Increase Speed of Freebayes

#58 cbird808 opened 5 years ago
11
awk program choice

#57 wirawan0 closed 4 years ago
1
update fastp cut_front and cut_tail args

#56 pdimens closed 5 years ago
0
parallel --env <function> throws error on some systems

#55 cbird808 opened 5 years ago
1
`getAssemblyInfo` is missing a closing `}`

#54 cbird808 closed 5 years ago
1
RPE Uniq Seqs Correct?

#53 cbird808 closed 5 years ago
0
Adaptive trimming of adapters with fastp

#52 chollenbeck closed 3 years ago
3
error in trimming

#51 nclowell closed 5 years ago
1
Changed the hard coded processor count for pearPM in line 1091 to $NUMProc to be consistent with the other invocations of pearPM

#50 relshire closed 5 years ago
0
PEAR is not accessible or licensed under a software iicense. Please consider substituting PANDAseq.

#49 relshire closed 5 years ago
1
Conda dDocent recipe has incorrect FreeBayes

#48 pdimens closed 5 years ago
1
cannot see how config file improperly configured

#47 nclowell closed 5 years ago
6
Change order of bwa mem parameters

#46 TomaszSuchan closed 5 years ago
1
LowerMemVersion

#45 jpuritz closed 5 years ago
1
early organization

#44 pdimens closed 5 years ago
3
Early steps of configured organization

#43 pdimens closed 5 years ago
0
"Checking for required software" not operating as expected

#42 mstuart1 closed 6 years ago
1
change trim logging

#41 pdimens closed 6 years ago
3