Closed dcopetti closed 5 years ago
Hi,
To get the input file for MizBee you have to run BlockDisplaySatsuma -i results-19vs19/satsuma_summary.chained.out -t asm-19g.chr.fasta -q asm-19g.chr.fasta > results-19vs19/mizbee.txt
. I also would like to use MizBee but unfortunately, I get the same problem because of:
Running seed pre-filter:
/satsuma2/bin/KMatch asm-19g.chr.fasta asm-19g.chr.fasta 11 results-19vs19/kmatch_results.k11 11 10 1; touch results-19vs19/kmatch_results.k11.finished
TIME_LOG: TIME_LOG: 1548288220566 - Loading array 1548288220566 - Loading array
Loading fasta asm-19g.chr.fasta into kmer array
Loading fasta asm-19g.chr.fasta into kmer array
Kmer array with 2773860504 elements created
TIME_LOG: 1548288288569 - Sorting array
Kmer array with 2773860504 elements created
TIME_LOG: 1548288289717 - Sorting array
Kmer array sorted
Kmer array sorted
terminate called after throwing an instance of 'std::length_error'
what(): vector::_M_default_append
Aborted
I created the below Singularity container in order to be sure that the error is not caused by our HPC environment. Running satsuma inside the container could confirm the same error message.
BootStrap: docker
From: ubuntu:16.04
%help
A container with satsuma
%post
apt-get update && apt-get -y upgrade
apt-get -y install \
build-essential \
cmake \
git
rm -rf /var/lib/apt/lists/*
apt-get clean
sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
dpkg-reconfigure --frontend=noninteractive locales && \
update-locale LANG=en_US.UTF-8
# install GSL
git clone https://github.com/bioinfologics/satsuma2.git
cd satsuma2
#sed -i.bak 's|set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -lpthread -std=c++14 -O3 -w")|set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -lpthread -std=c++14 -O0 -w")|' CMakeLists.txt
sed -i.bak 's|set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -lpthread -std=c++14 -O3 -w")|set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -lpthread -pthread -std=c++14 -O3 -w")|' CMakeLists.txt
mkdir build && cd build
cmake ..
make
mv /satsuma2/build/bin/* /satsuma2/bin
#echo -e '#!/bin/sh \necho "cd $1; $2" | qsub -V -l select=1:ncpus=${3}:mem=300G -N $5 \n' > /satsuma2/bin/satsuma_run.sh
chmod +x /satsuma2/bin/satsuma_run.sh
%environment
export SATSUMA2_PATH=/satsuma2/bin
export LANG=en_US.UTF-8
By any chance, did you find another way how to load any alignment into MizBee?
Thank you in advance,
Michal
Hi Michal, If you can send me the file 'asm-19g.chr.fasta' I'll try to replicate the error. Jon
Hi Jon, I have just sent you an email with the assembly.
Thank you for your help.
Michal
To summarise an offline conversation, this problem seems to be caused by the first KMatch step failing which means SatsumaSynteny doesn't generate the satsuma_summary.chained.out output file which in turn causes BlockDisplaySynteny to fail. We're looking into it further.
Hi @jonwright99, Were you able to get it running?
Michal
Hi @mictadlo, I've just pushed a fix which should solve your problem. The issue was caused by no unique 11-mers being found in your genome which caused KMatch to fail so the k11 output file was not generated. Best, Jon
Hi @jonwright99, Thank you for doing it. Everything works. Please find below the updated Singularity recipe:
BootStrap: docker
From: ubuntu:16.04
%help
A container with satsuma
%post
apt-get update && apt-get -y upgrade
apt-get -y install \
build-essential \
cmake \
git
rm -rf /var/lib/apt/lists/*
apt-get clean
sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
dpkg-reconfigure --frontend=noninteractive locales && \
update-locale LANG=en_US.UTF-8
# install GSL
git clone https://github.com/bioinfologics/satsuma2.git
cd satsuma2
mkdir build && cd build
cmake ..
make
mv /satsuma2/build/bin/* /satsuma2/bin
#echo '#!/bin/sh \necho "cd $1; $2" | qsub -V -l select=1:ncpus=${3}:mem=300G -N $5 \n' > /satsuma2/bin/satsuma_run.sh
chmod +x /satsuma2/bin/satsuma_run.sh
%environment
export SATSUMA2_PATH=/satsuma2/bin
export LANG=en_US.UTF-8
Thank you in advance,
Michal
@dcopetti, does this solve your problem as well or is this no longer an issue for you. Can I close this ticket?
@jonwright99 I did not have a chance to try it yet, within a few weeks I will need to re-run the same analysis. Let's close it for now, I will get back if there are issues. Thanks!
Hello, I was able to run SatsumaSynteny2 with two 3-Mb scaffolds (with -slaves 2 -threads 5 -sl_mem 50), now that I try to align 640 Mb of scaffolds vs a reference (single fasta) of 620, I get always errors like this:
even when the resources required are the lowest:
SatsumaSynteny2 -q LG4_scf.fa -t Hvul_chr4.fa -o chr4 -slaves 1 -threads 1 -sl_mem 20
What is the right setting to align my type of sequences?My next step would be to visualize such alignments: I see that the tool MizBee could be useful, but I don't find how to prepare the input files from Satsuma's output: is there a script or something? Also for the annotation would be great. thanks, Dario