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gt1 / daccord

d'accord is a non hybrid long read consensus program based on local de Bruijn graph assembly
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problem of .las file #2

Closed LeoChanW closed 7 years ago

LeoChanW commented 7 years ago

Hi ! I have installed Daligner(https://github.com/thegenemyers/DALIGNER), but I do not find how to get .las file. Should I get .las by DAMAPPER?

gt1 commented 7 years ago

You first need to create a Dazzler database (assuming your reads are in reads.fasta):

fasta2DB reads.db reads.fasta DBsplit -s192 -x1000 reads.db

fasta2DB and DBsplit are in the DAZZ_DB package (see https://github.com/thegenemyers/DAZZ_DB).

Then run DALIGNER on the database file with

HPC.daligner reads.db | bash

These steps require you to have the DAZZ_DB and DALIGNER programs in accessible via your PATH variable (i.e. you need to be able to run them without providing the full path of the binaries). DALIGNER has more options not shown here, please see the project page for what they are.

LeoChanW commented 7 years ago

Hi ! When I run daccord，there are some problems. (gmp library has installed by yum).

libmaus2::math::GmpFloat(): library is not built with gmp support /home/chw/libmaus2/lib/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x54)[0x7f1badeea924] /home/chw/libmaus2/lib/libmaus2.so.2(libmaus2::math::GmpFloat::GmpFloat(double, unsigned int)+0x36)[0x7f1badf7e726] daccord(computeOffsetLikely(unsigned long, double, double)+0x21e)[0x42cb1e] daccord(daccord(libmaus2::util::ArgParser const&, std::string const&, std::string const&, std::string const&)+0x1fc2)[0x436c92] daccord(main+0x126d)[0x4283dd] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f1bac3bcb35] daccord()[0x428c81]

gt1 commented 7 years ago

Hi,

sorry, this should be in the documentation. You need to use

--with-gmp

when configuring libmaus2 before building it.

LeoChanW commented 7 years ago

Daccord can run normally. Thanks for your help and patience！