faircloth-lab phyluce issues

faircloth-lab / phyluce

software for UCE (and general) phylogenomics

http://phyluce.readthedocs.org/

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issues

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Using the by-locus function when exploding monolithic fasta

#354 amateos1998 opened 2 weeks ago
1
Phyluce_probe_run_multiple_lastzs_sqlite creating empty lastz files, but no discernable errors.

#353 teaganme closed 2 weeks ago
5
phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed not functioning

#352 sbabbbie closed 3 weeks ago
2
Samples with multiple lane reads

#351 jb23590 opened 3 weeks ago
3
AttributeError: 'NoneType' object has no attribute 'groups'

#350 Genomics-Bhuwan opened 1 month ago
3
copy_and_build_index error in phyluce mapping

#349 kmontana13 opened 2 months ago
0
fix typo in phasing workflow

#348 stachyris opened 2 months ago
0
Issue with config file / names

#347 jb23590 closed 1 week ago
8
Error came as "ValueError: Sequences must all be the same length" when I run phyluce_align_seqcap_align

#346 Charmainehan closed 3 months ago
5
How to get joined_allele_sequences_all_samples.fasta

#345 emmajochim opened 4 months ago
4
phyluce_assembly_assemblo_spades [contig length issue]

#344 kimchafer opened 4 months ago
4
phyluce installation error at the conda env update --name phyluce-1.7.3-x86 ... stage

#343 kwinker opened 4 months ago
6
Adding SRR outgroups to the Phyluce pipeline

#342 bbessesen opened 5 months ago
20
phyluce_align_remove_locus_name_from_files does not clean names if output is fasta

#341 tauanajc closed 5 months ago
1
phyluce_probe_run_multiple_lastzs_sqlite issue

#340 jovana03 opened 6 months ago
1
illumiprocessor - unequal split-adapter-quality-trimmed read1 and read2

#339 jackson-roberts closed 6 months ago
2
phyluce_probe_run_multiple_lastzs_sqlite --probefile

#338 Jami5on opened 7 months ago
1
phyluce_assembly_match_contigs_to_probes - AttributeError: 'NoneType' object has no attribute 'groups'-NEW Issues

#337 jjinzhou closed 7 months ago
4
phyluce get match counts error

#336 Jami5on closed 7 months ago
0
phyluce_assembly_match_contigs_to_barcodes, OSError: lastz: b'Can\'t understand "/Users/rodolfoprobst/Library/CloudStorage/Box-Box/Myrmelachista_all"\n(my guess) perhaps you have too many sequence files in the command\n

#335 probstrodolfo opened 7 months ago
0
phyluce_assembly_get_match_counts, possible config issue

#334 bbessesen opened 7 months ago
9
WARNING - Did not clean all fastq/fasta files

#333 bbessesen opened 7 months ago
5
ConfigParser.NoSectionError: No section: 'names'

#332 Jami5on opened 8 months ago
3
Phyluce_alignment: All UCE loci dropped while using the --no-trim flag

#331 Samyuktha9624 closed 8 months ago
8
phyluce_snp_phase_uces yielding empty output files

#330 cLweinrich closed 8 months ago
2
sqlite error in "Determining locus presence in multiple genomes" step of Tutorial IV

#329 kautumn opened 8 months ago
0
Keep duplicates "contigs hitting multiple probes"

#328 sbabbbie opened 9 months ago
3
Help: Assembly stuck on "Processing contigs"

#327 chloejelley opened 9 months ago
3
"phyluce_ncbi_prep_uce_align_files_for_ncbi_targeted_locus_db" creates empty fsa and tbl files

#326 claudiavaga opened 9 months ago
1
Problems illuminaprocessor.conf

#325 TiagoBelintani closed 10 months ago
0
stampy: Error: Overfull hash table

#324 Ruben9161 opened 11 months ago
2
Error in the "phyluce_assembly_match_contigs_to_probes.job" step

#323 LauraGonzalezMozo opened 1 year ago
1
UnboundLocalError: local variable 'input' referenced before assignment

#322 51mystic closed 1 year ago
6
return match.groups()[0] AttributeError: 'NoneType' object has no attribute 'groups'

#321 51mystic closed 1 year ago
4
No such column error in phyluce_assembly_get_fastas_from_match_counts

#320 louisfnastasi opened 1 year ago
1
concatenate with character sets in Phyluce 1.7.1

#319 JennaMcCullough closed 1 year ago
3
Phyluce_assembly_explode_get_fastas_file UnboundLocalError

#318 louisfnastasi closed 1 year ago
6
Issues Installing Phyluce on M2 MacOS

#317 Anoplogaster closed 1 year ago
2
Problem with phyluce_assembly_match_contigs_to_probes for Trinity and Spades assemblies

#316 charbeez opened 1 year ago
2
Phasing snps fasta files

#315 nicolashazzi23 opened 1 year ago
13
Phyluce spaces assembly error?

#314 louisfnastasi closed 1 year ago
3
ERROR message "can't read /var/mail/Bio" running the Cleanup the genome sequences step from the Tutorial IV: Identifying UCE Loci and Designing Baits To Target Them

#313 Ruben9161 closed 11 months ago
2
NoneType

#312 ErikaGress opened 1 year ago
3
phyluce installation: dependencies missing?

#311 jbernot opened 1 year ago
9
error with "phyluce_align_get_only_loci_with_min_taxa"

#310 Gefsy closed 11 months ago
2
Phyluce pipeline - Illumiprocessor question

#309 louisfnastasi closed 1 year ago
3
Yet another illumiprocessor name error

#308 louisfnastasi closed 1 year ago
3
Concatenate alignments does not work with phylip-extended format alignments

#307 brantfaircloth opened 1 year ago
6
Ilumiprocessor config file issues

#306 NYX-PLUTO opened 1 year ago
2
Combined/merged sequence runs - best point to merge?

#305 eeeaston opened 1 year ago
3