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License: Other
Methods for the detection and assembly of novel sequence in high-throughput sequencing data
License: Other
Parsing command line...
Loading global state...
Checking input...
Estimating library size...
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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
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
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!
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
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
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.
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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