Hi,

I want to align paired-end RNA-seq using MAPSPLICE on a number of contigs obtained from the De-novo assembly. I am getting error : convert sam file to junctions failed. Please let me know if anybody has any suggestions regarding the same?

details are below :

[Mon Oct 21 12:09:53 2019] Beginning Mapsplice run (MapSplice v2.2.1)

[Mon Oct 21 12:09:53 2019] Bin directory: /home/prasoon/softwares/MapSplice-v2.2.1/bin/

[Mon Oct 21 12:09:53 2019] Preparing output location bbmap_repair_out_dj2k/

[Mon Oct 21 12:09:53 2019] Checking files or directory: bb_repair/R1.fq

[Mon Oct 21 12:09:53 2019] Checking files or directory: bb_repair/R2.fq

[Mon Oct 21 12:09:53 2019] Checking files or directory: dj2k//

[Mon Oct 21 12:09:53 2019] Checking Bowtie index files

[Mon Oct 21 12:09:53 2019] Inspecting Bowtie index files

[Mon Oct 21 12:09:53 2019] Checking reference sequence length

[Mon Oct 21 12:09:53 2019] Checking consistency of Bowtie index and reference sequence

[Mon Oct 21 12:09:53 2019] Checking read format

-----[Read Format: FASTQ]

-----[Read Type: Pair End]

-----[Total # Reads: 11241076]

-----[Max Read Length: 300]

-----[Min Read Length: 120]

-----[Max Quality Score: 71]

-----[Min Quality Score: 40]

-----[Quality Score Scale: Phred+33]

[Mon Oct 21 12:10:50 2019] Running MapSplice multi-thread

[Mon Oct 21 12:29:18 2019] Generating junctions from sam file

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

what(): basic_string::substr

[MapSplice Running Failed]

Error: convert sam file to junctions failed

command used : python mapsplice.py -o output_folder --min-map-len 20 -i 5 -I 8000 --del 2 --non-canonical-double-anchor --non-canonical-single-anchor -c contig_folder/ -1 raw_reads/R1.fq -2 raw_reads/R2.fq