Error: terminate called after throwing an instance of 'std::out_of_range'

[Klebsi]

Dear all,

I am running the following command:

cope -a For.fastq -b Rev.fastq -s 33 -m 3 -t output.freq.cz -f output.freq.cz.len -o Merged.fastq >cope.log 2>cope.error

and get an error when the read-file is loading:

loading kmerfreq table...
kmer freq table:
kmer_num node_num error_freq_num error_ratio suspicious_freq_num suspicious_ratio normal_freq_num normal_ratio repeat_freq_num repeat_ratio
1385464716 112135778 82607059 0.73667 11051915 0.0985583 12327050 0.10993 6149754 0.054842
finish loading kmer freq table!
Run time: 37s.
Begin read files and connect pairs...
Process pair reads number: 1000000
Process pair reads number: 2000000
Process pair reads number: 3000000
Connect reads finished!
starting to do cross connect for 3560968 pair reads
Use connected file to cross
Count pair kmer number...
Count kmer pair number: 1619676
loading pair kmer information!
starting to load pair kmer file...
loading kmer file finished! Totally load kmer pair number is: 1619676
sort pair kmers!
load hashset!
final hash set size is 8388733
load all reads to get cross reads
Begin load read file: Merged.fastq.connect.fq
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr

I don't know how to solve this and wonder if I need to adjust certain parameters to avoid this error.

Cheers!

[Binghang Liu]

Thanks Klebsi,
sorry for this bug of cope. -m 1 can be used to avoid this error. We'll try to fix it later.

Best,
bh