terminate called after throwing an instance of 'std::runtime_error' what(): Found unexpected delimiter C in fastq/fasta input

[goodcqzz]

A new bug log:

Crash report for vg v1.56.0 "Collalto" Stack trace (most recent call last) in thread 16259: #15 Object "", at 0xffffffffffffffff, in #14 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x21c85b3, in __clone #13 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x2121afa, in start_thread #12 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x20c438d, in gomp_thread_start #11 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0xecc7a4, in unsigned long vg::io::paired_for_each_parallel_after_waitvg::Alignment(std::function<bool (vg::Alignment&, vg::Alignment&)>, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>, unsigned long) [clone ._omp_fn.0] #10 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0xecdded, in std::_Function_handler<bool (vg::Alignment&, vg::Alignment&), vg::fastq_paired_two_files_for_each_parallel_after_wait(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>, unsigned long)::{lambda(vg::Alignment&, vg::Alignment&)#1}>::_M_invoke(std::_Any_data const&, vg::Alignment&, vg::Alignment&) #9 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x53793a, in vg::get_next_alignment_from_fastq(gzFile_s*, char*, unsigned long, vg::Alignment&) [clone .cold] #8 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x20db58d, in _Unwind_Resume #7 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x20daa0b, in _Unwind_RaiseException_Phase2 #6 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x20171c9, in __gxx_personality_v0 #5 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x20b16d8, in __cxa_call_terminate #4 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x2017a7b, in __cxxabiv1::__terminate(void (*)()) #3 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x5e8803, in __gnu_cxx::__verbose_terminate_handler() [clone .cold] #2 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x5eaf4b, in abort #1 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x20f6905, in raise #0 Object "/home/gaoch/miniconda3/envs/vg142/bin/vg", at 0x212345c, in __pthread_kill

[faithokamoto]

What command did you run, and what data did you use?

[adamnovak]

Are you sure your FASTQ doesn't have a C character where we expect a FASTQ delimiter?

[goodcqzz]

您运行了什么命令？使用了什么数据？ NGS data mapping to gbz using giraffe: vg giraffe -Z ${out}.giraffe.gbz -m ${out}.min -d ${out}.dist -f ${fq1} -f ${fq2} -t 7 > ${i}.gam

[goodcqzz]

您确定您的 FASTQ_没有_C我们期望的 FASTQ 分隔符字符吗？

Should be... fastq.gz file : sed -n l file_1.fq.gz

@SRR12827854.1 1/1$ NCCTTGCCAAGCTGGCAATGGTCTTTTTAGGCACCTATCACCGTCGTCTCTTAGAGCCTGATACAGTGA
AGACAATGCTGACACCTCTGTTTAAGTGCTCCACTGAATACTTTGCCAACAAGACTGGCACACCGTGGG
AGATTAACGAGC$ +$ #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF
FFFFFFFFFFFF$ @SRR12827854.2 2/1$ NAAAGGAAATACAGATAAATATCTAATGGAGTTCTTGATTAGCCCCAGATATCTGAGTCATAAACCCTC
CAGATCGCTAATTCAGTAGGTTTATATAAATAGTGCTATCTACTAGGTCATTGCCAGTGATTAATTAAT
TATGGATGGATC$ +$ #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFF
FFFF,FFFFFFF$