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Methods for the detection and assembly of novel sequence in high-throughput sequencing data

License: Other

CMake 0.78% Python 0.82% Awk 0.05% C++ 97.59% C 0.58% Shell 0.18%

anise_basil's Issues

Error: what(): Problem reading from VCF file.

Parsing command line...
Loading global state...
Checking input...
Estimating library size...
  estimation complete |                                                | 0/100000 [00:00:00/00:00:00]
  estimation complete |#####                                           | 10001/100000 [00:00:00/00:00:00]
  estimation complete |##########                                      | 20002/100000 [00:00:00/00:00:00]
  estimation complete |###############                                 | 30003/100000 [00:00:00/00:00:00]
  estimation complete |####################                            | 40004/100000 [00:00:00/00:00:00]
  estimation complete |#########################                       | 50005/100000 [00:00:00/00:00:00]
  estimation complete |#############################                   | 60006/100000 [00:00:00/00:00:00]
  estimation complete |##################################              | 70007/100000 [00:00:00/00:00:00]
  estimation complete |#######################################         | 80008/100000 [00:00:00/00:00:00]
  estimation complete |############################################    | 90009/100000 [00:00:00/00:00:00]
  estimation complete |################################################| 100000/100000 [00:00:00/00:00:00]
  estimation complete |################################################| 100000/100000 [00:00:00/00:00:00]
  library size: median=339, stdDev=92.6479
Perform preparation step...
  extracted sites |                                                | 0/47136 [00:00:00/00:00:00]
  extracted sites |#                                               | 1/47136 [00:00:02/27:25:14]
  extracted sites |#                                               | 1/47136 [00:00:02/27:25:15]
[……so many lines similar]
  extracted sites |##                                              | 1246/47136 [00:00:23/00:14:56]
  extracted sites |##                                              | 1247/47136 [00:00:23/00:14:55]
  extracted sites |##                                              | 1247/47136 [00:00:23/00:14:55]
terminate called after throwing an instance of 'std::runtime_error'
  what():  Problem reading from VCF file.

How has this happened? Seems weird to me

bad_alloc

Hello, I'm trying to use anise_basil to assemble some breakpoints around a duplication. I generated a basil.vcf file and am trying to run the anise step where I get the following error after it assembles 8/123 of the sites:

00:11/00:02:49]terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc

When I run it with the -v option, I get this error description:
Building Consensus...
Building alignment graph

fragments: 0

seqs: 295

progressive alignment...
build AG..
AG
numVertices = 295
numEdges = 0
componentLength.size() = 295
numComponents = 295
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted (core dumped)

I'm running it on a small (6 Mb) section of chr2, and the basil step detects 124 potential breakpoints, all of which I use in the anise assembly.
The machine I'm running it on has 16G, and anise seems to be using only a little over 1G, so it doesn't seem to be running out of memory.

Please let me know if you would like me to send my input files.

Thanks!

anise Segmentation fault

Basil found a very good candidate for our anticipated 2kb insert, but when I ran anise to assemble it, I get a segfault fairly quickly:

./anise_basil/build/bin/anise -ir Pseudomonas_aeruginosa_UCBPP-PA14_109.fa -im PA14_1_pe_trimmed.bam -iv PA14_1_pe_trimmed.basil.filtered.vcf -of PA14_1_pe_trimmed.basil.filtered.anise.vcf.fa
Parsing command line...
Loading global state...
Checking input...
Estimating library size...
  estimation complete |################################################| 100000/100000 [00:00:00/00:00:00]
  library size: median=344, stdDev=97.9034
Perform preparation step...
  extracted sites |                                                | 0/1 [00:00:06/00:00:00]Segmentation fault

I am using an index created by samtools:

samtools faidx Pseudomonas_aeruginosa_UCBPP-PA14_109.fa

Could that be the issue?

Thanks,
Rob

basil test fails due to ref.fa path

The test script for basil appears to compare the vcf files without accounting for a different value for the reference path:

diff /Users/rleach/local/miniconda3/conda-bld/anise_basil_1545249514348/work/test/01/basil.vcf /var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmp.z7rXj0Zi/basil.vcf
3c3
< ##reference=/home/manuel/Development/anise_basil/test/01/ref.fa
---
> ##reference=/Users/rleach/local/miniconda3/conda-bld/anise_basil_1545249514348/work/test/01/ref.fa

New release request

I was taking the liberty to create a conda recipe for anise_basil so that I could create a galaxy tool wrapper for basil. I use basil in a prokaryotic variant pipeline that I'm trying to turn into a galaxy workflow.

Anyway, it appears that there have been some significant changes since the last release that I wanted for the galaxy tool wrapper. I was able to use a regular revision hash to move forward, but a new release would be ideal. Do you think you could create one?

Also, a colleague pointed out that the license is a BSD3 license. (I don't work with licenses enough to recognize them by content.) I was thinking that it might be nice if the license was labeled as BSD3 in some way for numbskulls like me to know which type of license it is. :P Bioconda requires the license type in their config file and I didn't know what to put.

make error

I tried to install anise_basil according to the readme, but the make command fails due to seqan files not being found.
Here is a log file: build_anise_basil.txt

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