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LuoGroup2023 / DeChat

Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat
GNU General Public License v3.0
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Compilation error 1.0.1 on ubuntu 22.04 server LTS #8

Open melop opened 3 months ago

melop commented 3 months ago

Hello, I was trying to compile the bugfix 1.0.1 version on ubuntu 22.04. Towards the end of make it started with many of the following errors:

In file included from /public/software/dechat/DeChat-1.0.1/gatb-core/gatb-core/thirdparty/boost/config.hpp:61, from /public/software/dechat/DeChat-1.0.1/gatb-core/gatb-core/thirdparty/boost/type_index.hpp:17, from /public/software/dechat/DeChat-1.0.1/gatb-core/gatb-core/thirdparty/boost/variant/variant.hpp:21, from /public/software/dechat/DeChat-1.0.1/gatb-core/gatb-core/thirdparty/boost/variant.hpp:17, from /public/software/dechat/DeChat-1.0.1/gatb-core/gatb-core/src/gatb/tools/designpattern/impl/IteratorHelpers.hpp:32, from /public/software/dechat/DeChat-1.0.1/gatb-core/gatb-core/src/gatb/gatb_core.hpp:35, from /public/software/dechat/DeChat-1.0.1/src/dechat_1.hpp:7, from /public/software/dechat/DeChat-1.0.1/src/main.cpp:4: /usr/include/boost/smart_ptr/bad_weak_ptr.hpp:50:31: error: expected ‘;’ at end of member declaration 50 | char const what() const BOOST_NOEXCEPT_OR_NOTHROW BOOST_OVERRIDE | ^~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/shared_count.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/property_map/vector_property_map.hpp:14, from /usr/include/boost/property_map/property_map.hpp:602, from /usr/include/boost/graph/adjacency_list.hpp:27, from /public/software/dechat/DeChat-1.0.1/aligner-correct/lordec.h:12, from /public/software/dechat/DeChat-1.0.1/aligner-correct/correct_round1.h:5, from /public/software/dechat/DeChat-1.0.1/src/main.cpp:10: /usr/include/boost/smart_ptr/bad_weak_ptr.hpp:50:57: error: ‘BOOST_OVERRIDE’ does not name a type; did you mean ‘BOOST_VERSION’? 50 | char const what() const BOOST_NOEXCEPT_OR_NOTHROW BOOST_OVERRIDE

g++ version is g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0

melop commented 3 months ago

I forgot to add that this was probably because the system has a newer boost version installed. Although I created a conda environment with boost=1.67.0, cmake doesn't seem to pick up the boost from the conda environment - it keeps recognizing the system default boost. It would be nice if you can update the conda package instead.

LuoGroup2023 commented 2 months ago

I forgot to add that this was probably because the system has a newer boost version installed. Although I created a conda environment with boost=1.67.0, cmake doesn't seem to pick up the boost from the conda environment - it keeps recognizing the system default boost. It would be nice if you can update the conda package instead.

I'm very sorry I just saw your message. The Conda version of dechat should have been updated to version 1.0.1 last week. You can download and test it now!

melop commented 2 months ago

Hello, I updated to version 1.0.1 on conda, but now it encounters another error:

[Bloom: read solid kmers ] 100 % elapsed: 3 min 5 sec remaining: 0 min 0 sec cpu: 694.2 % mem: [9565, 9565, 9565] MB [Debloom: build extension ] 100 % elapsed: 6 min 16 sec remaining: 0 min 0 sec cpu: 3529.8 % mem: [9612, 9614, 9614] MB [Debloom: finalization ] 40 % elapsed: 62 min 30 sec remaining: 93 min 45 sec cpu: 351.3 % mem: [10402, 10813, 10859] MB HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:

000: /opt/conda/conda-bld/dechat_1717680464416/work/gatb-core/gatb-core/thirdparty/hdf5/src/H5Dio.c line 199 in H5Dread(): can't read data

major: Dataset
minor: Read failed

001: /opt/conda/conda-bld/dechat_1717680464416/work/gatb-core/gatb-core/thirdparty/hdf5/src/H5Dio.c line 601 in H5D__read(): can't read data

major: Dataset
minor: Read failed

002: /opt/conda/conda-bld/dechat_1717680464416/work/gatb-core/gatb-core/thirdparty/hdf5/src/H5Dchunk.c line 2259 in H5D__chunk_read(): unable to read raw data chunk

major: Low-level I/O
minor: Read failed

003: /opt/conda/conda-bld/dechat_1717680464416/work/gatb-core/gatb-core/thirdparty/hdf5/src/H5Dchunk.c line 3610 in H5D__chunk_lock(): unable to read raw data chunk

major: Low-level I/O
minor: Read failed

004: /opt/conda/conda-bld/dechat_1717680464416/work/gatb-core/gatb-core/thirdparty/hdf5/src/H5Fio.c line 118 in H5F_block_read(): read through page buffer failed

major: Low-level I/O
minor: Read failed

005: /opt/conda/conda-bld/dechat_1717680464416/work/gatb-core/gatb-core/thirdparty/hdf5/src/H5PB.c line 732 in H5PB_read(): read through metadata accumulator failed

major: Page Buffering
minor: Read failed

006: /opt/conda/conda-bld/dechat_1717680464416/work/gatb-core/gatb-core/thirdparty/hdf5/src/H5Faccum.c line 260 in H5F__accum_read(): driver read request failed

major: Low-level I/O
minor: Read failed

007: /opt/conda/conda-bld/dechat_1717680464416/work/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDint.c line 205 in H5FD_read(): driver read request failed

major: Virtual File Layer
minor: Read failed

008: /opt/conda/conda-bld/dechat_1717680464416/work/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDsec2.c line 725 in H5FD_sec2_read(): file read failed: time = Wed Jun 12 13:37:54 2024

, filename = 'reads_k35_s1.h5', file descriptor = 4, errno = 5, error message = 'Input/output error', buf = 0x7f268d053900, total read size = 72856, bytes this sub-read = 72856, bytes actually read = 18446744073709551615, offset = 0 major: Low-level I/O minor: Read failed EXCEPTION: HDF5 error (H5Dread), status -1 successful

chat_opt->outReadFile:corrected asm_opt->output_file_name:corrected asm_opt->max_ov_diff_ec:0.04 asm_opt->number_of_round:3 in assemble In ha_ft_gen /var/spool/slurmd/job245503/slurm_script: line 10: 3279864 Segmentation fault (core dumped) dechat -i allreads.filtered.1k.fq -o corrected -k 35 -d ngs_merged.fq.gz -t $CPU