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-   -   Problem creating index files from reference genome using miRDeep* (http://seqanswers.com/forums/showthread.php?t=67431)

newfie 04-07-2016 08:27 AM

Problem creating index files from reference genome using miRDeep*
 
Hi guys,

I am using miRDeep and i wanted to create index files to be used in miRDeep*. But i am getting an error every time i execute the command

This is their instructions on the mannual how to do it:

1. genome_test is a demo data directory. there are two fasta files chrM.fa and chrY.fa. you can put your own genome reference files in this directory chromosome by chromosome.
2. type command below:
> java -jar -Xmx4g build_bwt_idx.jar genome_test
for the option Xmx4g. you can change the amount based on how much memory your computer has
3. copy whole directory genome_test under miRDeep_star's genome directory. you can change genome_test if you like.

Now this is what i used in the command line:

java -jar ~/Downloads/build_bwt_idx_v31/build_bwt_idx.jar ~/Downloads/build_bwt_idx_v31/genome/genome_test

here is the output with error message:

Apr 07, 2016 6:12:07 PM build_bwt_idx.Build_bwt_idx main
SEVERE: null
java.io.FileNotFoundException: genome/home/amm/Downloads/build_bwt_idx_v31/genome/FM_profile.idx (No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:221)
at java.io.FileOutputStream.<init>(FileOutputStream.java:110)
at java.io.FileWriter.<init>(FileWriter.java:63)
at bowtie.create_BWT_Index.createIdx(create_BWT_Index.java:46)
at build_bwt_idx.Build_bwt_idx.main(Build_bwt_idx.java:34)

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I checked the path to the file, it is correct. Also, i omitted the Xmx4g option because i am using a super computer. Just for an exploratory purpose, i still used Xmx4g option but i get the very same error.

Anyone knows what this error means and how to rectify it?

Richard Finney 04-07-2016 08:38 AM

genome/home/amm/Downloads/build_bwt_idx_v31/genome/FM_profile.idx

Your goofing on the filename somehow.

Hardwire the full path or change directories.


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