[SolexaNewbie]

Hi,

I was doing on trial run for SpliceMap on my data and got this error message after Bowtie mapping:

Genereating mapping file!...
Total mapping index creation section execution time: 541.607 s.
Total Mapping section time: 11970.7 s.
Running SpliceMap on /home/bowtie/chr1.fa ...
COMMAND: ./bin/SpliceMap test.cfg /home/bowtie/chr1.fa
ERROR: fork failed

Has anyone else had this problem / knows of a fix?

Thank you.

[john_mu]

Hi,

I was doing on trial run for SpliceMap on my data and got this error message after Bowtie mapping:

Genereating mapping file!...
Total mapping index creation section execution time: 541.607 s.
Total Mapping section time: 11970.7 s.
Running SpliceMap on /home/bowtie/chr1.fa ...
COMMAND: ./bin/SpliceMap test.cfg /home/bowtie/chr1.fa
ERROR: fork failed

Has anyone else had this problem / knows of a fix?

Thank you.

Hi,

Does the example data set in the tutorial work?

[SolexaNewbie]

Hi John,

Thank you very much for your prompt reply. Yes, I've just run the tutorial and all went well. I will try moving the chr1.fa (downloaded from UCSC) to the genome folder used in the tutorial.

[john_mu]

Hi John,

Thank you very much for your prompt reply. Yes, I've just run the tutorial and all went well. I will try moving the chr1.fa (downloaded from UCSC) to the genome folder used in the tutorial.

I hope that works.

I'm trying to think why that might be the case.. If it still doesn't work
could you email me the log files as described in

http://www.stanford.edu/group/wonglab/SpliceMap/contact.html

You can directly send to me at johnmu (at) stanford.edu

Sorry for the trouble!

John Mu

[saathe]

Hi I am very new to RNA-seq analysis. But I need to complete the mapping of my data using SpliceMap. I am not able to edit the run.cfg file and I am getting the following error
""ls: cannot access /cluster/rnaseq/genome/hg18/chr*.fa: No such file or directory
ERROR: I found no chromosomes, please check the genome_dir (/cluster/rnaseq/genome/hg18/) and the chromosome_wildcard (chr*.fa)"".
Could anyone tell me how to correct the same? I put the index files like hg18_c.1.ebwt
etc and the .fa files in different folders in the working directory.