[genomicist]

Thank you, I have removed the spaces in the read names and re-running MapSplice now. There is hope!

[dsobral]

I'm having the same error.

I am using Ensembl Chromosomes, and they have "false" spaces in their name (which actually correspond to the description of the fasta).
eg. >Uextra dna:chromosome chromosome:BDGP5:Uextra:1:29004656:1

I've removed that extra part... let's hope it works now.

[wmaassen]

I run into the same problem as repinementer. It gives an error in which it states that in needs the islands.gff file in the output folder. However, I cannot find this file in the output folder. Have more people encountered this problem?

Input:
python ~/MapSplice_1.15.2_macos/bin/mapsplice_segments.py -u ~/read1.fastq,~/read2.fastq -c ~/database/human_per_chromosome -B ~/MapSplice_1.15.2_macos/bowtie-0.12.7/index/h_sapiens_37_asm -Q fq —paired

Output:
[Tue Apr 5 11:49:10 2016] Beginning Mapsplice run (v1.15.2)
------------------------------------------------------
bin directory: [/Users/kmaassen/projects/mapsplice/MapSplice_1.15.2_macos_2/bin/]
[Tue Apr 5 11:49:10 2016] Checking for chromosomes files or directory
[Tue Apr 5 11:49:10 2016] Checking for chromosomes files or directory passed
[Tue Apr 5 11:49:10 2016] Checking for Bowtie index files
[Tue Apr 5 11:49:10 2016] check reads format
[Tue Apr 5 11:49:16 2016] merge paired end reads remove short
[Tue Apr 5 11:49:40 2016] Converting bowtie mapped to SAM format
[Tue Apr 5 11:49:40 2016] divide reads
[Tue Apr 5 11:52:07 2016] Mapping reads against h_sapiens_37_asm with Bowtie
[Tue Apr 5 12:00:36 2016] reads all chromo sizes
[Tue Apr 5 12:00:52 2016] map splice_search
[Tue Apr 5 12:00:58 2016] Aligning spliced reads
cannot open input file mapsplice_out/tmp/islands.gff
[FAILED]
Error: Spliced read alignment failed