A problem about the download of the human genome in defuse

Question

[jiagehao]

Dear friends,

My name is Jia LI, I am using defuse to detect fusion genes in cancers and used the following command line to download human genome.

perl create_reference_dataset.pl -c config.txt

The genome I got is:

defuse.dna.chromosomes.10.fa defuse.dna.chromosomes.17.fa defuse.dna.chromosomes.2.fa defuse.dna.chromosomes.9.fa defuse.dna.chromosomes.11.fa defuse.dna.chromosomes.18.fa defuse.dna.chromosomes.3.fa defuse.dna.chromosomes.MT.fa defuse.dna.chromosomes.12.fa defuse.dna.chromosomes.19.fa defuse.dna.chromosomes.4.fa defuse.dna.chromosomes.X.fa defuse.dna.chromosomes.13.fa defuse.dna.chromosomes.1.fa defuse.dna.chromosomes.5.fa defuse.dna.chromosomes.Y.fa defuse.dna.chromosomes.14.fa defuse.dna.chromosomes.20.fa defuse.dna.chromosomes.6.fa Homo_sapiens.GRCh37.69.dna.chromosomes.fa defuse.dna.chromosomes.15.fa defuse.dna.chromosomes.21.fa defuse.dna.chromosomes.7.fa Homo_sapiens.GRCh37.69.gtf defuse.dna.chromosomes.16.fa defuse.dna.chromosomes.22.fa defuse.dna.chromosomes.8.fa repeats.txt.gz

Then I used defuse.pl to call fusion genes, however I got the errors here.

Job command with nonzero return code Job output: Running on node3
Error: Required file /home/jli/defuse-0.6.2/Reference/defuse.cdna.fa does not exist

I downloaded the genome twice and had the same problem. Does anyone have a suggestion? thank you so much.

Answer 1

[onuralp]

Hey Jia Li,

First, make sure that you have the cDNA fasta file defuse.cdna.fa exists in the following folder: /home/jli/defuse-0.6.2/Reference/

If it does not, then some error must have occurred when downloading the reference files. (it is likely that the connection cut off before downloading EST files)

In any case, inspect the config.txt to see that all paths are defined correctly, and then try running create_reference_dataset.pl again to download all necessary files to perform the analysis.

Otherwise, it should all work ok. Here are the instructions if you need them.