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HaploKit / Strainline

Full-length de novo viral haplotype reconstruction from noisy long reads
GNU General Public License v3.0
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run fails on Nenopore data #3

Open gianfilippo opened 2 years ago

gianfilippo commented 2 years ago

Hi,

I tried your code on a Nanopore sample I have. I converted FASTQ to FASTA and used it as input.

I get the following in the log file [V] args[0]=daccord [V] args[1]=-t20 [V] args[2]=reads.\052las [V] args[3]=reads.dam PosixFdInput(reads.*las,0): No such file or directory

daccord-0.0.10-release-20170526170720-x86_64-etch-linux-gnu/bin/../lib/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x55)[0x2b824904df95] daccord(libmaus2::exception::LibMausException::LibMausException()+0x20)[0x42c180] daccord-0.0.10-release-20170526170720-x86_64-etch-linux-gnu/bin/../lib/libmaus2.so.2(libmaus2::aio::PosixFdInput::PosixFdInput(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, int)+0x205)[0x2b8249023e25] accord-0.0.10-release-20170526170720-x86_64-etch-linux-gnu/bin/../lib/libmaus2.so.2(libmaus2::aio::PosixFdInputStreamFactory::constructUnique(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)+0x22a)[0x2b824902d6fa] daccord(libmaus2::aio::InputStreamFactoryContainer::constructUnique(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)+0xc3)[0x432513] daccord-0.0.10-release-20170526170720-x86_64-etch-linux-gnu/bin/../lib/libmaus2.so.2(libmaus2::aio::InputStreamInstance::InputStreamInstance(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)+0x7b)[0x2b82490f1c5b] daccord()[0x4511f3] daccord()[0x41cbb9] daccord()[0x40ea68] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b824c2fd555] daccord()[0x410512]

DerekLake commented 1 year ago

I also have this exact issue. Any insight on how to fix this?