New version of MapSplice error

[repinementer]

I just tested new version of Mapsplice and it throwed the following error

]$ 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

[mendl7]

I am getting the same error from my attempt to use this software. It appears the islands.gff file is not being created in the output directory. Please help.

[mendl7]

bumpbumpbump

[nilshomer]

bumpbumpbump

Warning #2 on "the bumping".

[greenshell]

Chromosome file name and first line of fasta line not consistent might cause mapsplice_search to fail to generate island file. For example if the chromosome file name is "chr1.fa" the first line in fasta file should be >chr1.

Please contact mapsplice (at) netlab.uky.edu for bug reports.

[areyes]

I had the same problem, it was solved by moving all the other .fa files from the directory

[areyes]

i mean the ones that are not fasta files corresponding to a chromosome

[cat]

Hi there!
I'm getting the same error message and I tried all the suggestions that have been mentioned but nothing worked. The first line within my chromosome files is the name of the file, in my chromosome folder are the chromosome files and nothing else. I work with the D. melaogaster genome so I thought that I may have got another release than the bowtie's reference sequence. But again it didn't work. Please help me

[greenshell]

Are there any other warning in the log file?

Can you send
unspliced_mapped_segments|unspliced_mapped_segments.sorted
unspliced_mapped_reads
divided_reads.fa
chrom_sizes

to
mapsplice (at) netlab.uky.edu?

Hi there!
I'm getting the same error message and I tried all the suggestions that have been mentioned but nothing worked. The first line within my chromosome files is the name of the file, in my chromosome folder are the chromosome files and nothing else. I work with the D. melaogaster genome so I thought that I may have got another release than the bowtie's reference sequence. But again it didn't work. Please help me

[burt]

I'm having the same problem too.

[greenshell]

Can you send first 10K line of

unspliced_mapped_segments|unspliced_mapped_segments.sorted
unspliced_mapped_reads
divided_reads.fa
chrom_sizes

to
mapsplice (at) netlab.uky.edu?

Most of the error is because the input file format is not correct, e.g. read name contain blank space, etc.

In the latest version of MapSplice, input file format checking is added.
If chromosome file format is not correct, warning message will be printed and it will try to convert chromosome file to correct format
If read file format is not correct, error message will be printed and exit

[genomicist]

I have the same problem. I run the latest version of MapSplice (v1.15.1), but still get the same error message: "cannot open input file mapsplice_Mm666_75bp_noribo/tmp/islands.gff [FAILED]" . Does anyone have a solution?

[greenshell]

I have the same problem. I run the latest version of MapSplice (v1.15.1), but still get the same error message: "cannot open input file mapsplice_Mm666_75bp_noribo/tmp/islands.gff [FAILED]" . Does anyone have a solution?

Can you send first 10K line of

unspliced_mapped_segments|unspliced_mapped_segments.sorted
unspliced_mapped_reads
divided_reads.fa
chrom_sizes

to
mapsplice (at) netlab.uky.edu?

1.15.2 added checking of blank space in read name

[genomicist]

I do have a blank in my read names - is it what is causing this problem?

[greenshell]

Yes, the format constraint is required in manual