Ecosyste.ms: Issues

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GitHub / faircloth-lab/phyluce issues and pull requests

#309 - Phyluce pipeline - Illumiprocessor question

Issue - State: open - Opened by louisfnastasi over 1 year ago - 3 comments

#308 - Yet another illumiprocessor name error

Issue - State: open - Opened by louisfnastasi over 1 year ago - 3 comments

#306 - Ilumiprocessor config file issues

Issue - State: open - Opened by tobihays over 1 year ago - 2 comments

#305 - Combined/merged sequence runs - best point to merge?

Issue - State: open - Opened by eeeaston over 1 year ago - 3 comments

#303 - Mapping against a Trinity genome assembly?

Issue - State: open - Opened by Trinity2018 over 1 year ago

#301 - phyluce_assembly_extract_contigs_to_barcodes

Issue - State: open - Opened by jovana03 over 1 year ago - 1 comment

#300 - non-UCE probes, slice UCE probes from genome

Issue - State: closed - Opened by crcardenas over 1 year ago - 9 comments

#299 - Using harvested genome sequences in downstream analyses

Issue - State: closed - Opened by alexfranzen over 1 year ago - 3 comments

#298 - phyluce_probe_run_multiple_lastzs_sqlite error/bug

Issue - State: closed - Opened by crcardenas over 1 year ago - 5 comments

#297 - phyluce not installing on macOS aarch64

Issue - State: closed - Opened by macrinl over 1 year ago - 4 comments

#296 - phyluce failed to find reads during phasing workflow

Issue - State: open - Opened by andreluizherpeto over 1 year ago - 3 comments
Labels: Bug

#294 - exploding the monolithic fasta by locus?

Issue - State: closed - Opened by lcgraber over 1 year ago - 3 comments

#293 - phasing workflow: insufficient memory for Java Runtime Environment to continue

Issue - State: closed - Opened by jbernst over 1 year ago - 5 comments

#292 - phyluce_snp_bwa_multiple_align

Issue - State: closed - Opened by TiagoBelintani over 1 year ago - 1 comment

#291 - Using the --continue option from spades

Issue - State: open - Opened by aureliendejode almost 2 years ago - 1 comment

#290 - Problem installing phyluce using miniconda

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

#289 - KeyError with phyluce_probe_slice_sequence_from_genomes

Issue - State: closed - Opened by sunandan-dasgupta almost 2 years ago - 13 comments

#288 - Mapping of reads (phyluce_snp_bwa_multiple_align)

Issue - State: open - Opened by irbinveliz almost 2 years ago - 1 comment

#287 - Illumiprocessor not removing adapters and barcodes?

Issue - State: closed - Opened by jbernst almost 2 years ago - 30 comments

#286 - Phyluce downloading error

Issue - State: open - Opened by Nomada-atra almost 2 years ago - 2 comments

#285 - Obtaining a final .vcf file with ambiguities for diploid organisms

Issue - State: open - Opened by marianamazzochi almost 2 years ago - 5 comments

#284 - <jemalloc>: Error in malloc(): out of memory

Issue - State: open - Opened by marianamazzochi about 2 years ago - 5 comments

#283 - ValueError: Invalid alphabet, 'DNA'

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

#281 - Phyluce on Apple M-series Processors

Issue - State: closed - Opened by coliverbrown about 2 years ago - 12 comments
Labels: Bug

#280 - Error during install

Issue - State: closed - Opened by rdriver about 2 years ago - 3 comments

#279 - internal trimming - no such file or directory

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

#278 - could not find conda environment: phylum-1.7.1

Issue - State: open - Opened by luzeocho over 2 years ago - 1 comment

#277 - phyluce_assembly_assemblo_spades memory issues with tmp directory location

Issue - State: closed - Opened by nhamilton857 over 2 years ago - 4 comments

#276 - uce probe for plant

Issue - State: closed - Opened by conniecl over 2 years ago

#275 - Upscaling phyluce for large datasets

Issue - State: open - Opened by karlyhiggins over 2 years ago - 1 comment

#274 - Issue in "phyluce_assembly_get_match_counts"

Issue - State: closed - Opened by claudiavaga over 2 years ago - 1 comment

#273 - phyluce_assembly_assemblo_spades no contig.fasta file

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

#272 - Error in "phyluce_assembly_match_contigs_to_probes"

Issue - State: closed - Opened by kq1986 over 2 years ago - 3 comments

#271 - Error in workflow mapping

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

#270 - Add "phylip-relaxed" to phyluce_align_extract_taxa_from_alignments

Issue - State: open - Opened by brantfaircloth over 2 years ago
Labels: Bug

#269 - contig correction changing bcftools flags

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

#268 - Naming issue - Illumiprocessor config file

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

#267 - How to know which version of phyluce is installed on a computer?

Issue - State: closed - Opened by Ruben9161 almost 3 years ago - 1 comment

#266 - using phyluce_assembly_match_contigs_to_probes on phased sequences

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

#265 - error in Final data matrices

Issue - State: closed - Opened by luishdez35 almost 3 years ago - 3 comments

#264 - Workflows: phasing.conf contig paths

Issue - State: closed - Opened by StephenBaca almost 3 years ago - 7 comments

#263 - Issue in the assembly

Issue - State: closed - Opened by luishdez35 almost 3 years ago - 1 comment

#262 - Problem with phyluce_assembly_get_match_counts

Issue - State: closed - Opened by ratonvaquero almost 3 years ago - 6 comments

#261 - phyluce_align_get_only_loci_with_min_taxa

Issue - State: closed - Opened by solenopsis1840 almost 3 years ago - 8 comments

#260 - Issue in Quality Control

Issue - State: open - Opened by luishdez35 almost 3 years ago - 2 comments

#258 - phyluce cannot get fasta files for samples

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

#257 - phyluce_assembly_assemblo_spades memory allocation issue on cluster

Issue - State: open - Opened by mprebus about 3 years ago - 4 comments

#255 - phasing workflow output question

Issue - State: closed - Opened by Motikuko about 3 years ago - 6 comments

#254 - An error occurred during installation

Issue - State: open - Opened by qilu521 about 3 years ago

#253 - SNP calling

Issue - State: closed - Opened by leonvarhan about 3 years ago - 2 comments

#251 - gblocks error - bad CPU type in executable

Issue - State: open - Opened by Otorongo1 about 3 years ago - 12 comments

#250 - SPades assembly issue

Issue - State: closed - Opened by hutumpyancha about 3 years ago - 13 comments

#248 - mapping workflow error

Issue - State: open - Opened by mprebus about 3 years ago - 1 comment

#247 - unmix fasta reads errors

Issue - State: open - Opened by michaelforthman about 3 years ago - 2 comments

#246 - Missing input file when doing a workflow mapping

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

#245 - Logging error phyluce_align_get_only_loci_with_min_taxa

Issue - State: closed - Opened by jbernst about 3 years ago - 2 comments

#244 - phyluce_probe_run_multiple_lastzs_sqlite v1.7 issues

Issue - State: open - Opened by michaelforthman about 3 years ago - 2 comments

#243 - Adjusting Mafft parameters, gappy alignments

Issue - State: open - Opened by StephenBaca over 3 years ago - 2 comments

#242 - remove_duplicate_hits_from_probes stuck for days

Issue - State: open - Opened by sihellem over 3 years ago - 1 comment

#241 - gatk IndelRealigner causing core dumps

Issue - State: open - Opened by BirdmanRidesAgain over 3 years ago - 5 comments

#240 - issue spades: Expected assembly files were not found in output.

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

#239 - I am new with Phyluce and I need your help, please

Issue - State: open - Opened by luishdez35 over 3 years ago - 6 comments

#238 - Add missing data designators

Issue - State: closed - Opened by jkorstia over 3 years ago - 15 comments

#237 - phyluce_align_add_missing_data_designators fails to run

Issue - State: closed - Opened by shofmon88 over 3 years ago - 2 comments

#236 - How to symlink extracted UCE loci from genomes into contigs file

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

#235 - Problem installing phyluce 1.7.1

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

#234 - Adding Barcode+Adapter Removed SRA Sequences into Phyluce

Issue - State: open - Opened by alexkrohn over 3 years ago - 4 comments

#232 - Easy Way to Update Contig Symlinks to New Path?

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

#231 - phyluce_probe_get_multi_merge_table syntax error

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

#230 - Fix location of triCas1.fasta

Pull Request - State: closed - Opened by Zachary-Muscavitch over 3 years ago

#229 - made directory structure consistent

Pull Request - State: closed - Opened by Zachary-Muscavitch over 3 years ago

#228 - Picard Dependency Issue - CleanSam truncates .bam files

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

#227 - RAxML Output has Many Loci with Only Undetermined Values

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

#225 - phyluce_align_get_only_loci_with_min_taxa removes too many alignments

Issue - State: closed - Opened by alexkrohn over 3 years ago - 5 comments

#224 - "phyluce_snp_bwa_multiple_align" command missing in phyluce 1.7.1

Issue - State: open - Opened by jasonleebrown over 3 years ago - 2 comments

#223 - phyluce_snp_convert_vcf_to_structure invalid literal

Issue - State: open - Opened by heather340 over 3 years ago - 4 comments

#222 - phyluce_workflow phasing issue: java.lang.OutOfMemoryError: Java heap space

Issue - State: open - Opened by lpnunez over 3 years ago - 8 comments

#221 - phyluce_probe_slice_sequence_from_genomes: KeyError: 'chr1'

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

#220 - phyluce_align_concatenate_alignments not found

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

#219 - Problem with phyluce_probe_run_multiple_lastzs_sqlite

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

#218 - Fix version header when not in git

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

#208 - Illumiprocessor - naming issue

Issue - State: closed - Opened by MaxTBC about 4 years ago - 13 comments

#201 - phyluce_align_get_only_loci_with_min_taxa gives fewer loci than expected

Issue - State: closed - Opened by claudiavaga about 4 years ago - 9 comments

#173 - Allow extra specifiers in UCE names (e.g., to imply a probeset namespace)

Issue - State: open - Opened by wmaddisn about 5 years ago
Labels: Enhancement

#163 - Issue running Quality control step in Tutorial 1

Issue - State: closed - Opened by BenjaminBlanchard over 5 years ago - 8 comments

#158 - ConfigParser.NoSectionError: No section: 'names'

Issue - State: closed - Opened by liugang9988 over 5 years ago - 23 comments

#157 - Trimming alignment drops all loci

Issue - State: closed - Opened by heather340 over 5 years ago - 10 comments

#156 - phyluce_align_seqcap_align returns error

Issue - State: closed - Opened by mchj74 over 5 years ago - 1 comment

#143 - Places where PHYLUCE needs to be faster

Issue - State: open - Opened by brantfaircloth almost 6 years ago - 8 comments
Labels: Enhancement