I just tested new version of Mapsplice and it throwed the following error
Code:
]$ python bin/mapsplice_segments.py MapSplice.cfg [Fri Aug 20 17:29:24 2010] Beginning Mapsplice run (v1.13.6.1) ----------------------------------------------- bin directory: [/home/bogugk/rnaseq/software/MapSplice_1.13.6.1/bin/] [Fri Aug 20 17:29:24 2010] Preparing output location /home/bogugk/rnaseq/Human_CD4TCell_RNASEQ_data/MapSplice_Outputs/ [Fri Aug 20 17:29:24 2010] Checking for chromosomes files or directory [Fri Aug 20 17:29:24 2010] Checking for Bowtie index files [Fri Aug 20 17:29:24 2010] merge paired end reads [Fri Aug 20 17:29:24 2010] Converting bowtie mapped to SAM format [Fri Aug 20 17:29:24 2010] divide reads [Fri Aug 20 17:31:30 2010] Mapping reads against hg18 with Bowtie [Fri Aug 20 19:29:10 2010] reads all chromo sizes [Fri Aug 20 19:29:44 2010] mapsplice_search [Fri Aug 20 19:32:13 2010] Aligning spliced reads cannot open input file /home/bogugk/rnaseq/Human_CD4TCell_RNASEQ_data/MapSplice_Outputs/tmp/islands.gff [FAILED] Error: Spliced read alignment failed Traceback (most recent call last): File "bin/mapsplice_segments.py", line 5823, in ? sys.exit(main()) File "bin/mapsplice_segments.py", line 5278, in main search_whole_chromo) File "bin/mapsplice_segments.py", line 1023, in call_mapsplice_segment exit(1) TypeError: 'str' object is not callable
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