David E. Condon

Hello, I'm processing some files that were output by afterQC, but I'm double checking with FastQC, and it looks like the output from AfterQC is truncated: ``` Failed to process...

"split chromosome" after sorting

1

I'm running bcftools 1.15.1 on Linux 4.18.0-372.16.1.el8_6.x86_64 on Red Hat 8.6 (Ootpa) with gcc version 8.5.0 I am running bcftools in a series of commands first I run `bcftools sort`...

The warning ""die" used instead of "croak" at line" should be turned off when the user has the "Devel::Confess" package loaded. `Devel::Confess` provides the necessary stack tracing that you don't...

I'm printing data in Perl6 with `Data::Printer` which is a spectacular package, but am trying to alter parameters and am not able to: For example, I want HG00112 { gained_site...

Pasta fails with homologs and muscle -> no sequences

4

I'm running PASTA thus: ` python pasta/run_pasta.py --num-cpus=6 --aligner=HOMOLOGS --merger=MUSCLE --tree-estimator=RAXML -i simulated_reads/x.fa --alignment-suffix=HOMOLOGS.MUSCLE.RAXML.x -j HOMOLOGS.MUSCLE.RAXML.x` and getting this output: ``` PASTA INFO: Reading input sequences from 'simulated_reads/x.fa'... PASTA INFO:...

Why aren't Saté & Pasta listed in the "External Tools" aligners?

1

I'm confused by the available aligners with the Pasta GUI, why isn't Saté listed as a possible aligner? Also https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424971/ seems to indicate that PASTA is another aligner itself, instead...

**Describe the bug** SyncTex is enabled on Preferences. However, when clicking on the source code on the left, nothing changes in the Preview Pane. When clicking on the Preview Pane,...

model.fit(train_dataset, nb_epoch=100) fails during DeepChem tutorial

6

## 🐛 Bug ## To Reproduce Steps to reproduce the behavior: import deepchem as dc ``` >>> dc.__version__ '2.5.0' >>> tasks, datasets, transformers = dc.molnet.load_delaney(featurizer='GraphConv') >>> >>> train_dataset, valid_dataset, test_dataset...

`Not an ARRAY reference` when using `filter`

3

I'm attempting to read a CSV file: ``` #!/usr/bin/env perl use 5.042; no source::encoding; use warnings FATAL => 'all'; use autodie ':default'; use Text::CSV_XS 'csv'; use Devel::Confess 'color'; use DDP...