Ecosyste.ms: Issues

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

GitHub / faircloth-lab/phyluce issues and pull requests

#362 - Error running phyluce_ncbi_prep_uce_align_files_for_ncbi_targeted_locus_db

Issue - State: open - Opened by tomgiarla about 1 month ago - 3 comments

#361 - phyluce_assembly_assemblo_spades failing for some sequences

Issue - State: open - Opened by antnette about 1 month ago - 1 comment

#360 - UCE tutorial II: error with phyluce_snp_bwa_multiple_align

Issue - State: closed - Opened by v-ensenat about 1 month ago - 2 comments

#359 - UCE names do not match error in uce-tutorial when using abyss assembler

Issue - State: open - Opened by mlosada323 about 2 months ago - 2 comments

#357 - "Cannot find the a fasta file" error

Issue - State: open - Opened by franztastic 2 months ago - 1 comment

#356 - How much sequencing data do I need?

Issue - State: open - Opened by BrigidaGallone 3 months ago - 2 comments

#354 - Using the by-locus function when exploding monolithic fasta

Issue - State: open - Opened by amateos1998 3 months ago - 1 comment

#351 - Samples with multiple lane reads

Issue - State: open - Opened by jb23590 4 months ago - 3 comments

#350 - AttributeError: 'NoneType' object has no attribute 'groups'

Issue - State: open - Opened by Genomics-Bhuwan 5 months ago - 3 comments

#349 - copy_and_build_index error in phyluce mapping

Issue - State: open - Opened by kmontana13 5 months ago

#348 - fix typo in phasing workflow

Pull Request - State: open - Opened by stachyris 5 months ago

#347 - Issue with config file / names

Issue - State: closed - Opened by jb23590 5 months ago - 8 comments

#345 - How to get joined_allele_sequences_all_samples.fasta

Issue - State: open - Opened by emmajochim 7 months ago - 4 comments

#344 - phyluce_assembly_assemblo_spades [contig length issue]

Issue - State: open - Opened by kimchafer 7 months ago - 4 comments

#342 - Adding SRR outgroups to the Phyluce pipeline

Issue - State: open - Opened by bbessesen 8 months ago - 20 comments

#340 - phyluce_probe_run_multiple_lastzs_sqlite issue

Issue - State: open - Opened by jovana03 9 months ago - 1 comment

#338 - phyluce_probe_run_multiple_lastzs_sqlite --probefile

Issue - State: open - Opened by Jami5on 10 months ago - 1 comment

#336 - phyluce get match counts error

Issue - State: closed - Opened by Jami5on 10 months ago

#334 - phyluce_assembly_get_match_counts, possible config issue

Issue - State: open - Opened by bbessesen 10 months ago - 9 comments

#333 - WARNING - Did not clean all fastq/fasta files

Issue - State: open - Opened by bbessesen 11 months ago - 5 comments

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

Issue - State: open - Opened by Jami5on 11 months ago - 3 comments

#331 - Phyluce_alignment: All UCE loci dropped while using the --no-trim flag

Issue - State: closed - Opened by Samyuktha9624 11 months ago - 8 comments

#330 - phyluce_snp_phase_uces yielding empty output files

Issue - State: closed - Opened by cLweinrich 11 months ago - 2 comments

#328 - Keep duplicates "contigs hitting multiple probes"

Issue - State: open - Opened by sbabbbie 12 months ago - 3 comments

#327 - Help: Assembly stuck on "Processing contigs"

Issue - State: open - Opened by chloejelley about 1 year ago - 3 comments

#325 - Problems illuminaprocessor.conf

Issue - State: closed - Opened by TiagoBelintani about 1 year ago

#324 - stampy: Error: Overfull hash table

Issue - State: open - Opened by Ruben9161 about 1 year ago - 2 comments

#323 - Error in the "phyluce_assembly_match_contigs_to_probes.job" step

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

#322 - UnboundLocalError: local variable 'input' referenced before assignment

Issue - State: closed - Opened by 51mystic over 1 year ago - 6 comments

#320 - No such column error in phyluce_assembly_get_fastas_from_match_counts

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

#319 - concatenate with character sets in Phyluce 1.7.1

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

#318 - Phyluce_assembly_explode_get_fastas_file UnboundLocalError

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

#317 - Issues Installing Phyluce on M2 MacOS

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

#315 - Phasing snps fasta files

Issue - State: open - Opened by nicolashazzi23 over 1 year ago - 13 comments

#314 - Phyluce spaces assembly error?

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

#312 - NoneType

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

#311 - phyluce installation: dependencies missing?

Issue - State: open - Opened by jbernot over 1 year ago - 9 comments

#310 - error with "phyluce_align_get_only_loci_with_min_taxa"

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

#309 - Phyluce pipeline - Illumiprocessor question

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

#308 - Yet another illumiprocessor name error

Issue - State: closed - 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 almost 2 years ago

#301 - phyluce_assembly_extract_contigs_to_barcodes

Issue - State: open - Opened by jovana03 almost 2 years ago - 1 comment

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

Issue - State: closed - Opened by crcardenas almost 2 years ago - 9 comments

#299 - Using harvested genome sequences in downstream analyses

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

#298 - phyluce_probe_run_multiple_lastzs_sqlite error/bug

Issue - State: closed - Opened by crcardenas almost 2 years ago - 5 comments

#297 - phyluce not installing on macOS aarch64

Issue - State: closed - Opened by macrinl almost 2 years ago - 4 comments

#296 - phyluce failed to find reads during phasing workflow

Issue - State: closed - Opened by andreluizherpeto almost 2 years ago - 6 comments
Labels: Bug

#295 - phyluce_assembly_match_contigs_to_probes stopped working

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

#294 - exploding the monolithic fasta by locus?

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

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

Issue - State: closed - Opened by jbernst almost 2 years ago - 5 comments

#292 - phyluce_snp_bwa_multiple_align

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

#289 - KeyError with phyluce_probe_slice_sequence_from_genomes

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

#288 - Mapping of reads (phyluce_snp_bwa_multiple_align)

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

#287 - Illumiprocessor not removing adapters and barcodes?

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

#286 - Phyluce downloading error

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

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

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

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

Issue - State: open - Opened by marianamazzochi over 2 years ago - 8 comments

#283 - ValueError: Invalid alphabet, 'DNA'

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

#281 - Phyluce on Apple M-series Processors

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

#280 - Error during install

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

#274 - Issue in "phyluce_assembly_get_match_counts"

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

#273 - phyluce_assembly_assemblo_spades no contig.fasta file

Issue - State: closed - Opened by karlyhiggins almost 3 years ago - 5 comments

#272 - Error in "phyluce_assembly_match_contigs_to_probes"

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

#271 - Error in workflow mapping

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

#270 - Add "phylip-relaxed" to phyluce_align_extract_taxa_from_alignments

Issue - State: open - Opened by brantfaircloth almost 3 years ago
Labels: Bug

#269 - contig correction changing bcftools flags

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

#266 - using phyluce_assembly_match_contigs_to_probes on phased sequences

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

#265 - error in Final data matrices

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

#264 - Workflows: phasing.conf contig paths

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

#263 - Issue in the assembly

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