Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / MikkelSchubert/paleomix issues and pull requests

#57 - Error encountered when setting maximum gap opens to 2

Issue - State: open - Opened by KrisTabb 5 months ago - 5 comments

#56 - Paleomix output reads folder no fastq reads

Issue - State: open - Opened by xuefenfei712 12 months ago - 2 comments

#55 - Duplicated reads error

Issue - State: closed - Opened by laneatmore 12 months ago - 3 comments

#54 - BWA terminated by SIGKILL, PALEOMIX in BAM pipline

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

#53 - Receieved a NodeError while running the pipeline

Issue - State: open - Opened by farahwar about 1 year ago - 1 comment

#52 - Error with trimming SE adapters from sample

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

#51 - Errors running node

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

#50 - conda environment perpetually solving during installation

Issue - State: closed - Opened by laurenhamm over 1 year ago - 6 comments

#49 - BWA backtrack additional options added to samse, not aln

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

#48 - Phylo pipeline "unknown command"

Issue - State: closed - Opened by 974ben almost 2 years ago - 2 comments

#47 - similar bams with rescale and non rescale

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

#46 - Issue When Employing `RegionsOfInterest`.

Issue - State: closed - Opened by g-pacheco over 2 years ago - 6 comments

#45 - Paleomix can not find picard even though it is there

Issue - State: closed - Opened by themudo over 2 years ago - 8 comments

#44 - biobambam2 instead of picard-tools?

Issue - State: open - Opened by sameoldmike over 3 years ago - 10 comments

#43 - Should the .rmdup.collapsed.bam and .rmdup.normal.bam be merged?

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

#42 - A problem of PALEOMIX 2.0.0-alpha documentation

Issue - State: closed - Opened by YoungLU1 over 3 years ago - 2 comments

#41 - BOWTIE2 errors in the pipeline

Issue - State: closed - Opened by ArchaeologyRoz over 3 years ago - 8 comments

#40 - About the MinQuality setting

Issue - State: closed - Opened by ztang040 almost 4 years ago - 6 comments

#39 - checkpointing

Issue - State: closed - Opened by kimh11 about 4 years ago - 2 comments

#36 - "Could not retrieve index file"

Issue - State: closed - Opened by ab08028 over 4 years ago - 1 comment

#34 - thank you, but this message appears with PALEOMIX v.1.2.14 too

Issue - State: closed - Opened by flaviode over 4 years ago - 3 comments

#33 - Java issue with an updated openjdk version

Issue - State: closed - Opened by flaviode over 4 years ago - 1 comment

#32 - Add conda instructions to documentation

Pull Request - State: closed - Opened by jfy133 over 4 years ago - 1 comment

#31 - [info] conda instructions for paleomix

Issue - State: closed - Opened by jfy133 over 4 years ago - 1 comment

#30 - Error running mapDamage in example bam_pipeline

Issue - State: closed - Opened by Rhinogradentia over 4 years ago - 2 comments

#29 - Alignment to sequence variation graph?

Issue - State: open - Opened by nwales almost 5 years ago - 1 comment

#28 - Paleomix expecting gatk.jar to be in a specific folder?

Issue - State: closed - Opened by gtrichard about 5 years ago - 3 comments

#27 - pip install seems broken

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

#26 - GATK error

Issue - State: closed - Opened by deFerran about 5 years ago - 2 comments

#25 - "Positional data is too large for BAM format"

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

#24 - paleomix doesnot work

Issue - State: closed - Opened by xuefenfei712 about 5 years ago - 8 comments

#23 - GATKv4 not supported?

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

#22 - bam_pipeline error

Issue - State: closed - Opened by denise0593 over 5 years ago - 7 comments

#21 - Paleomix bam_pipeline error

Issue - State: closed - Opened by nsmt89 over 5 years ago - 1 comment

#20 - Phylo pipeline example not working

Issue - State: closed - Opened by teepean about 6 years ago - 1 comment

#19 - Issue running the example bam_pipeline

Issue - State: closed - Opened by ldutoit about 6 years ago - 2 comments

#18 - Trimming first 6-8 bp of read 1

Issue - State: open - Opened by nwales over 6 years ago - 2 comments

#17 - documentation for paloemix phylo pipeline

Issue - State: open - Opened by siriusb-nox over 6 years ago - 1 comment

#16 - write-config

Issue - State: closed - Opened by blondie5125 over 6 years ago - 2 comments

#15 - Please switch to Python3

Issue - State: closed - Opened by tillea almost 7 years ago - 22 comments

#14 - Tox tests do not work

Issue - State: closed - Opened by tillea over 7 years ago

#13 - Failure in build time test

Issue - State: closed - Opened by tillea over 7 years ago - 1 comment

#12 - Make vcf_to_fasta.py work with VCFs containing haploid genotype calls.

Pull Request - State: closed - Opened by grahamgower over 7 years ago - 1 comment

#11 - Please try to drop code copy of pyyaml

Issue - State: closed - Opened by tillea almost 8 years ago - 8 comments

#10 - Soft clipped reads are not correctly deduplicated

Issue - State: closed - Opened by grahamgower about 8 years ago - 6 comments

#9 - time elapsed reset by using function keys

Issue - State: closed - Opened by ginolhac over 8 years ago - 2 comments
Labels: question

#8 - Update setup.py

Pull Request - State: closed - Opened by MikkelSchubert over 8 years ago

#7 - skip adapter-trimming

Issue - State: closed - Opened by ginolhac about 9 years ago - 2 comments

#6 - paleomix spawning zombies, waiting in futex_

Issue - State: closed - Opened by grahamgower over 9 years ago - 5 comments

#5 - 'empty header' error

Issue - State: closed - Opened by beeso018 over 9 years ago - 4 comments

#4 - Change in default tmp dir?

Issue - State: closed - Opened by schae234 over 9 years ago - 2 comments
Labels: question

#3 - fix help text for the coverage tool

Pull Request - State: closed - Opened by ginolhac over 9 years ago

#2 - picard tools are not individual jars anymore

Issue - State: closed - Opened by ginolhac over 9 years ago - 3 comments

#1 - Passing path to reference sequence containing spaces

Issue - State: closed - Opened by simonohanlon101 over 10 years ago - 2 comments