rvaser / ra Goto Github PK

Hi,

Could you provide us with information about how long and what memory and disk space the assembly for model species such as E coli, yeast, fruit fly and human take?

Cheers,

Hi,

I am trying to assemble ~60X nanopore data of 1.5Gb genome, but always failed at minimap2 stage. I tried to generate paf/sam file using minimap2 independently outside Ra successfully, so any advices would be appreciated.

Log below:
.
.
[M::worker_pipeline::60395.41131.30] mapped 52375 sequences
[M::worker_pipeline::60561.05931.29] mapped 50263 sequences
[M::worker_pipeline::60717.325*31.29] mapped 52061 sequences
[ERROR] failed to write the results
[Ra::run] preconstruction overlap stage

Hello Robert,

I would like to test your assembler on my Linux system. When compiling the tool, I come across some errors:
After:

git clone --recursive https://github.com/rvaser/ra.git ra
cd ra
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make

Errors:

In file included from /mydir/software/pool/ra/vendor/rala/src/pile.cpp:11:0:
/mydir/software/pool/ra/vendor/rala/src/overlap.hpp:77:31: error: ‘vector’ in namespace ‘std’ does not name a template type
     bool transmute(const std::vector<std::unique_ptr<Pile>>& piles,
                               ^~~~~~
/mydir/software/pool/ra/vendor/rala/src/overlap.hpp:77:37: error: expected ‘,’ or ‘...’ before ‘<’ token
     bool transmute(const std::vector<std::unique_ptr<Pile>>& piles,
                                     ^
/mydir/software/pool/ra/vendor/rala/src/overlap.hpp:80:26: error: ‘vector’ in namespace ‘std’ does not name a template type
     bool trim(const std::vector<std::unique_ptr<Pile>>& piles);
                          ^~~~~~
/mydir/software/pool/ra/vendor/rala/src/overlap.hpp:80:32: error: expected ‘,’ or ‘...’ before ‘<’ token
     bool trim(const std::vector<std::unique_ptr<Pile>>& piles);
                                ^
make[2]: *** [vendor/rala/CMakeFiles/rala.dir/src/pile.cpp.o] Error 1
make[1]: *** [vendor/rala/CMakeFiles/rala.dir/all] Error 2
make: *** [all] Error 2

Could you please help me deal with this problem? Thanks in advance.

Hi Robert,

I have installed RA following instructions without errors.
But when I tried to run the following command:
python /sw/ra/build/bin/ra -t 16 -x ont ont.fastq.gz > ra.fa

I get an empty assembly fasta file and the following message:
[Ra::run] preconstruction overlap stage
[M::mm_idx_gen::185.227*2.22] collected minimizers
[Ra::exit] warning: unable to clean work directory!

Any idea?

Thanks in advance.
Valentine

Hi,
I tried to use Ra on a Nanopore dataset (in fasta) but it crashes during the layout stage. I tried to launch manually the rala command and got a segmentation fault. Ra is working well on some other datasets, do you have an idea of something I could do to fix this crash ?

Hi
I ran RA for a plant genome with genome size 1G and 50X nanopore reads.
The program has been running for 1700cpu hours and still running. The log last update was 6 days ago.
How many cpu hours will ra take for an 1G genome? Is there any way to increase speed？

The log file is as follows:

...
[Ra::run] layout stage
[rala::Graph::initialize] loaded sequences
[rala::Graph::initialize] loaded overlaps
[rala::Graph::preprocess] dataset coverage median = 337
[rala::Graph::preprocess] processed chimeric sequences
[rala::Graph::initialize] number of prefiltered sequences = 453302
[rala::Graph::initialize] elapsed time = 1132638.85608 s

Hello, I'm trying to run Ra, however I keep getting an error that the option p doesn't exist for rala as shown below:

[M::main] Version: 2.14-r894-dirty
[M::main] CMD: /bin/minimap2 -t 15 -x ava-pb greysnapper.all.subreads.fasta greysnapper.all.subreads.fasta
[M::main] Real time: 9741.901 sec; CPU: 134577.332 sec; Peak RSS: 40.247 GB
[Ra::run] preconstruction stage
/bin/rala: invalid option -- 'p'

The only changes I made to the Ra script generated after compilation is changing the paths of racon rala and minimap2 to the ones compiled to /bin/ as shown here:

class Ra:

    __minimap = '/bin/minimap2'
    __rala = '/bin/rala'
    __racon = '/bin/racon'

which leads me to believe the issue may be in this section:

     # preconstruction
        eprint('[Ra::run] preconstruction stage')

        rala_params = [Ra.__rala, '-t', str(self.threads)]
        if (self.include_unused):
            rala_params.extend(['-u'])
        rala_params.extend(['-p'])     #right here?
        rala_params.extend([self.tgs_sequences, overlaps])

Do you have any information regarding what may be going on?

Hi,
RA has failed with the following error message

unequal lengths in sequence and overlap file for sequence with id 508204 without any further log message.

Here are the last few lines of the log-file:

[M::main] CMD: /disk2/nguinkal/ra/vendor/minimap2/minimap2 -t 100 -x ava-pb /disk2/nguinkal/mnt/winpro/I3-NGS-Daten/NGS-Fisch/Zander-Project_2017_2020/RawData/Zander_SMRT_Sequel/SMRT_Sequel-Pooled/zander_pooled.subreads.renamed.fasta /disk2/nguinkal/mnt/winpro/I3-NGS-Daten/NGS-Fisch/Zander-Project_2017_2020/RawData/Zander_SMRT_Sequel/SMRT_Sequel-Pooled/zander_pooled.subreads.renamed.fasta
[M::main] Real time: 12065.368 sec; CPU: 868149.797 sec
[Ra::run] preconstruction stage
[rala::Graph::initialize] loaded sequences
[rala::Overlap::transmute] error: unequal lengths in sequence and overlap file for sequence with id 508204!

I am running RA on Debian based linux Workstation.
I have no clue what is causing that bug. Thanks for any hints.
Cheers,
Julien

Hello RA team,

Installed RA following instructions without error.
However when i try to run the following command...
python ../../scripts/ra/build/bin/ra -t 16 -x pb pacbio.fasta
I get the following error...
[Ra::run] preconstruction overlap stage
[Ra::run] error: unable to run minimap2!
[Ra::exit] warning: unable to clean work directory!

Any advice?
I've tried changing how Minimap2 is called but it's still not working.

Brian

Hi Robert,

I have used Ra for the assembly of a small plant, with ONT and Illumina data. My ONT data is not as long as one would wish, but I am still trying to assemble a draft. Anyway, I tried Ra with both datasets and I got a genome size of 13 Mb, while I am expecting something more close to 280 Mb.

I would like to know if there are some parameters that I can tweak or something I can do to rerun Ra and get a different assembly than the one I got.

Thanks in advance.

Hello Robert,

When I installed ra tool, I came across some errors:
After:

Errors:
[ 2%] Building CXX object vendor/rala/vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o In file included from /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:9: /home/chifa/ra/vendor/rala/vendor/thread_pool/include/thread_pool/thread_pool.hpp:15:18: error: future: No such file or directory /home/chifa/ra/vendor/rala/vendor/thread_pool/include/thread_pool/thread_pool.hpp:16:18: error: atomic: No such file or directory In file included from /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:9: /home/chifa/ra/vendor/rala/vendor/thread_pool/include/thread_pool/thread_pool.hpp:65: error: expected type-specifier /home/chifa/ra/vendor/rala/vendor/thread_pool/include/thread_pool/thread_pool.hpp:65: error: expected initializer /home/chifa/ra/vendor/rala/vendor/thread_pool/include/thread_pool/thread_pool.hpp:101: error: ISO C++ forbids declaration of ‘atomic’ with no type /home/chifa/ra/vendor/rala/vendor/thread_pool/include/thread_pool/thread_pool.hpp:101: error: invalid use of ‘::’ /home/chifa/ra/vendor/rala/vendor/thread_pool/include/thread_pool/thread_pool.hpp:101: error: expected ‘;’ before ‘<’ token /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp: In member function ‘void thread_pool::Semaphore::wait()’: /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:38: error: expected primary-expression before ‘[’ token /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:38: error: expected primary-expression before ‘]’ token /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp: In constructor ‘thread_pool::ThreadPool::ThreadPool(uint32_t)’: /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:47: error: ‘terminate_’ was not declared in this scope /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp: In destructor ‘thread_pool::ThreadPool::~ThreadPool()’: /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:56: error: ‘terminate_’ was not declared in this scope /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:60: error: expected initializer before ‘:’ token /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:63: error: expected primary-expression before ‘}’ token /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:63: error: expected ‘;’ before ‘}’ token /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:63: error: expected primary-expression before ‘}’ token /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:63: error: expected ‘)’ before ‘}’ token /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:63: error: expected primary-expression before ‘}’ token /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:63: error: expected ‘;’ before ‘}’ token /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp: In static member function ‘static void thread_pool::ThreadPool::worker_thread(thread_pool::ThreadPool*)’: /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:70: error: ‘class thread_pool::ThreadPool’ has no member named ‘terminate_’ /home/chifa/ra/vendor/rala/vendor/thread_pool/src/thread_pool.cpp:81: error: ‘class thread_pool::ThreadPool’ has no member named ‘terminate_’ make[2]: *** [vendor/rala/vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o] Error 1 make[1]: *** [vendor/rala/vendor/thread_pool/CMakeFiles/thread_pool.dir/all] Error 2 make: *** [all] Error 2

Could you help me identify the problem? Many thanks.

Hi,

I am writing to ask if we can provide the Ra the minimap2 paf file in addition to the fastq files? So Ra can skip the alignment stage and get onto the next stages.

This option would be great because we are running on a server which restrict running time for 96 hours. I think the minimap2 stage can be finished successfully but not sure if the next stages can be done by then.