core dumped

[oscarvargash]

I am getting a core dumped in the current version 1.10.07 (2017-12-14), see text below. I have tried an older version and the older version is functional - Version: 1.9.12 (2017-07-07).

performing the analysis in a Ubuntu machine

seqyclean -qual 20 20 -minlen 25 -polyat -c Illumina_contaminants.fa -1 4guan_S102_L008_R1_001.fastq.gz -2 4guan_S102_L008_R2_001.fastq.gz -o filtered/04guan_S 4guan_S102_L008_R1_001.fastq.gz ====================Parameters======================== Version: 1.10.07 (2017-12-14) --------------------Basic parameters-------------------- Provided data files : PE1: 4guan_S102_L008_R1_001.fastq.gz, PE2: 4guan_S102_L008_R2_001.fastq.gz Adapters trimming: YES. Vector screening: NO Contaminants screening: YES. File_of_contaminants: Illumina_contaminants.fa K-mer size for contaminants: 15 Quality trimming: YES Maximum error: 20 Maximum error at ends: 20 Poly A/T trimming: YES cdna =10 c_err = 3 crnq = 50 Duplicates removal: NO --------------------Output files-------------------- Output prefix: filtered/04guan_S Report files: filtered/04guan_S_PE1_Report.tsv, filtered/04guan_S_PE2_Report.tsv PE1 file: filtered/04guan_S_PE1.fastq PE2 file: filtered/04guan_S_PE2.fastq Single-end reads: filtered/04guan_S_SE.fastq --------------------Other parameters-------------------- Maximum number of mismatches allowed in alignment: 7 Minimum read length to accept: 25 New to old-style Illumina headers: NO Old-style Illumina: NO Q-value: 33 ====================Starting the process==================== Parsing screening file Illumina_contaminants.fa Running the Illumina cleaning process... Processing files: 4guan_S102_L008_R1_001.fastq.gz, 4guan_S102_L008_R2_001.fastq.gz terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 99) > this->size() (which is 51) Aborted (core dumped)

[izhbannikov]

Thanks for letting me know. Will fix this asap. Ilya