faircloth-lab phyluce issues

faircloth-lab / phyluce

software for UCE (and general) phylogenomics

http://phyluce.readthedocs.org/

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phyluce_snp_bwa_multiple_align issue

#150 mprebus closed 5 years ago
2
phyluce_align_get_only_loci_with_min_taxa not giving the correct number of taxa in output

#149 camilocalderon closed 3 years ago
8
phyluce_assembly_get_trinity_coverage_for_uce_loci raise IOError("Picard metrics file for {} has more than two lines".format(sample))

#148 KNx5 closed 3 years ago
12
Update tutorial-three.rst

#147 milag6 closed 5 years ago
1
phyluce_snp_bwa_multiple_align fails to merge BAMs - File "/anaconda2/envs/phyluce/bin/phyluce_snp_bwa_multiple_align", line 193, in <module> main() File "/anaconda2/envs/phyluce/bin/phyluce_snp_bwa_multiple_align", line 182, in main bam = picard.merge_two_bams(log, sample, sample_dir, bam, bam_se) File "/anaconda2/envs/phyluce/lib/python2.7/site-packages/phyluce/picard.py", line 124, in merge_two_bams os.remove(bam) OSError: [Errno 2] No such file or directory:

#146 andreluizherpeto closed 3 years ago
4
phyluce_assembly_get_fastas_from_match_counts error - sequences longer than expected

#145 wjaratlerdsiri closed 5 years ago
1
phyluce_align_get_smilogram_from_alignments

#144 mcfaddenlab closed 5 years ago
1
Places where PHYLUCE needs to be faster

#143 brantfaircloth opened 5 years ago
8
phyluce_assembly_get_trinity_coverage_for_uce_loci issue

#142 michael-branstetter closed 3 years ago
3
phyluce_assembly_get_trinity_coverage issue related to gatk

#141 michael-branstetter closed 3 years ago
2
Howto change abyss contig fasta headers using a bash script

#140 wjaratlerdsiri closed 5 years ago
1
Add missing data designators

#139 discipleofdarwin closed 5 years ago
4
"harvesting in silico UCEs"

#138 KNx5 closed 5 years ago
3
jellyfish: not found

#137 lucper closed 5 years ago
2
conda install -c bioconda phyluce

#136 lucper closed 5 years ago
4
create a partitioned data file

#135 GideonPisanty closed 5 years ago
4
sre_constants.error: nothing to repeat

#134 discipleofdarwin closed 5 years ago
2
phyluce_assembly_get_trinity_coverage

#133 GideonPisanty closed 3 years ago
5
Can't run script phyluce_snp_get_from_uce_alignments.py

#132 Ptero64 closed 5 years ago
1
Link needs updating in tutorial three

#131 mkweskin closed 3 years ago
1
Memory issue when running phyluce_assembly_assemblo_spades

#130 jphruska closed 3 years ago
5
Missing information for all loci using internal trimming/gblocks?

#129 ghost closed 6 years ago
20
Matching contigs to barcodes - No SQLite database generated?

#128 TomSemple closed 4 years ago
3
Error while using ABySS to assemble SRA sequences

#127 JLWilliAnts closed 3 years ago
0
can't upgrade python from 3.6 to 3.7

#126 hhuhhu closed 6 years ago
6
Assembly (velvet/abyss) not being able to detect fastq.gz?

#125 ghost closed 6 years ago
1
Make config file input case sensitive in phyluce_align_convert_one_align_to_another

#124 brantfaircloth closed 6 years ago
0
install Phyluce on Mac 10.12.6

#123 jxzhangzhang closed 3 years ago
1
IO Error There are not appropriate files in dir

#122 camilocalderon closed 6 years ago
2
Illumiprocessor does not run no output is generated

#121 lostcode-sam closed 5 years ago
8
Trimming the start of reads

#120 Cryptamydros closed 3 years ago
2
Trinity 2013 fails in the latest phyluce version (IOError: Neither Trinity.fasta nor trinity.log were found in output.)

#119 nnbuainain closed 3 years ago
20
configue file in Tutorial IV： Identifying UCE Loci and Designing Baits To Target Them

#118 KaiqiangLiu closed 5 years ago
0
Error: Could not parse --min-ac g -> phyluce_snp_phase_uces

#117 jdhenaos closed 6 years ago
3
What parameters are used for Trimmomatic in illumiprocessor

#116 jojoventure closed 6 years ago
1
phyluce_assembly_get_fastas_from_match_counts: AttributeError

#115 TomSemple closed 6 years ago
4
error report in phyluce_align_explode_alignments

#114 nnbuainain closed 6 years ago
2
Phasing UCE data - phasing mapped reads wrote 1 allele

#113 nnbuainain closed 6 years ago
7
GATK jar file not found

#112 kwinker closed 3 years ago
16
Porting phyluce to Python 3.6

#111 brantfaircloth closed 3 years ago
2
Porting phyluce to bioconda

#110 brantfaircloth closed 6 years ago
4
Possible issues with miniconda: phyluce_ commands don't seem to work.

#109 drwhitehouse closed 6 years ago
4
Improve trinity error reporting

#108 brantfaircloth closed 3 years ago
5
phasing uce snps

#107 mcfaddenlab closed 6 years ago
7
An error in running 'phyluce_probe_get_tiled_probes'

#106 ClearloveMiao closed 3 years ago
4
phyluce_align_format_nexus_files_for_mrbayes

#105 lphunt closed 3 years ago
0
phyluce_snp_bwa_multiple_align error - unable to locate gatk tools

#104 bryansmclean closed 6 years ago
3
Problem running Cloudforest

#103 lphunt closed 6 years ago
0
phyluce_assembly_get_trinity_coverage spades issue

#102 mcfaddenlab closed 6 years ago
10
Missing executables from snp phasing workflow

#101 ericcrandall closed 6 years ago
14

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