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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phyluce installation error at the conda env update --name phyluce-1.7.3-x86 ... stage

#343 kwinker opened 9 hours ago
0
Adding SRR outgroups to the Phyluce pipeline

#342 bbessesen opened 1 week ago
3
phyluce_align_remove_locus_name_from_files does not clean names if output is fasta

#341 tauanajc closed 2 weeks ago
1
phyluce_probe_run_multiple_lastzs_sqlite issue

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

#339 jackson-roberts closed 1 month ago
2
phyluce_probe_run_multiple_lastzs_sqlite --probefile

#338 Jami5on opened 2 months ago
1
phyluce_assembly_match_contigs_to_probes - AttributeError: 'NoneType' object has no attribute 'groups'-NEW Issues

#337 jjinzhou closed 2 months ago
4
phyluce get match counts error

#336 Jami5on closed 2 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 2 months ago
0
phyluce_assembly_get_match_counts, possible config issue

#334 bbessesen opened 2 months ago
7
WARNING - Did not clean all fastq/fasta files

#333 bbessesen opened 2 months ago
5
ConfigParser.NoSectionError: No section: 'names'

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

#331 Samyuktha9624 closed 3 months ago
8
phyluce_snp_phase_uces yielding empty output files

#330 cLweinrich closed 3 months ago
2
sqlite error in "Determining locus presence in multiple genomes" step of Tutorial IV

#329 kautumn opened 3 months ago
0
Keep duplicates "contigs hitting multiple probes"

#328 sbabbbie opened 4 months ago
3
Help: Assembly stuck on "Processing contigs"

#327 chloejelley opened 4 months ago
3
"phyluce_ncbi_prep_uce_align_files_for_ncbi_targeted_locus_db" creates empty fsa and tbl files

#326 claudiavaga opened 4 months ago
1
Problems illuminaprocessor.conf

#325 TiagoBelintani closed 5 months ago
0
stampy: Error: Overfull hash table

#324 Ruben9161 opened 7 months ago
2
Error in the "phyluce_assembly_match_contigs_to_probes.job" step

#323 LauraGonzalezMozo opened 7 months ago
1
UnboundLocalError: local variable 'input' referenced before assignment

#322 51mystic closed 7 months ago
6
return match.groups()[0] AttributeError: 'NoneType' object has no attribute 'groups'

#321 51mystic closed 7 months ago
4
No such column error in phyluce_assembly_get_fastas_from_match_counts

#320 louisfnastasi opened 8 months ago
1
concatenate with character sets in Phyluce 1.7.1

#319 JennaMcCullough closed 8 months ago
3
Phyluce_assembly_explode_get_fastas_file UnboundLocalError

#318 louisfnastasi closed 8 months ago
6
Issues Installing Phyluce on M2 MacOS

#317 Anoplogaster closed 8 months ago
2
Problem with phyluce_assembly_match_contigs_to_probes for Trinity and Spades assemblies

#316 charbeez opened 9 months ago
2
Phasing snps fasta files

#315 nicolashazzi23 opened 9 months ago
6
Phyluce spaces assembly error?

#314 louisfnastasi closed 8 months 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 7 months ago
2
NoneType

#312 ErikaGress opened 9 months ago
3
phyluce installation: dependencies missing?

#311 jbernot opened 10 months ago
9
error with "phyluce_align_get_only_loci_with_min_taxa"

#310 Gefsy closed 6 months ago
2
Phyluce pipeline - Illumiprocessor question

#309 louisfnastasi closed 8 months ago
3
Yet another illumiprocessor name error

#308 louisfnastasi closed 8 months ago
3
Concatenate alignments does not work with phylip-extended format alignments

#307 brantfaircloth opened 11 months ago
6
Ilumiprocessor config file issues

#306 NYX-PLUTO opened 11 months ago
2
Combined/merged sequence runs - best point to merge?

#305 eeeaston opened 1 year ago
3
Insufficient memory fir the java runtime environment to continue. NMAP- Native memory allocation failed

#304 Sarangkrr opened 1 year ago
0
Mapping against a Trinity genome assembly?

#303 Trinity2018 opened 1 year ago
0
phasing workflow failed - one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!

#302 andreluizherpeto closed 1 year ago
3
phyluce_assembly_extract_contigs_to_barcodes

#301 jovana03 opened 1 year ago
1
non-UCE probes, slice UCE probes from genome

#300 crcardenas closed 1 year ago
9
Using harvested genome sequences in downstream analyses

#299 alexfranzen closed 1 year ago
3
phyluce_probe_run_multiple_lastzs_sqlite error/bug

#298 crcardenas closed 1 year ago
5
phyluce not installing on macOS aarch64

#297 macrinl closed 1 year ago
4
phyluce failed to find reads during phasing workflow

#296 andreluizherpeto opened 1 year ago
3
phyluce_assembly_match_contigs_to_probes stopped working

#295 marianamateos opened 1 year ago
1
exploding the monolithic fasta by locus?

#294 lcgraber closed 1 year ago
3