The soapfuse running problem

Question

[syxbestmayer]

(ln -sf /home/share/databases/transcript.fa /home/share/databases/transcript_index_bwa/transcript.fa) && (/home/share/tool/SOAPfuse-v1.26/source/bin/aln_bin/bwa index /home/share/databases/transcript_index_bwa/transcript.fa)
[bwa_index] Pack FASTA... [bns_fasta2bntseq] zero length sequence. Abort!
sh: line 1: 15710 Aborted                 (core dumped) ( /home/share/tool/SOAPfuse-v1.26/source/bin/aln_bin/bwa index /home/share/databases/transcript_index_bwa/transcript.fa )
[bwa_index] Pack FASTA... [bns_fasta2bntseq] zero length sequence. Abort!
sh: line 1: 15717 Aborted                 (core dumped) ( /home/share/tool/SOAPfuse-v1.26/source/bin/aln_bin/bwa index /home/share/databases/transcript_index_bwa/transcript.fa )
[bwa_index] Pack FASTA... [bns_fasta2bntseq] zero length sequence. Abort!
sh: line 1: 15722 Aborted                 (core dumped) ( /home/share/tool/SOAPfuse-v1.26/source/bin/aln_bin/bwa index /home/share/databases/transcript_index_bwa/transcript.fa )
[bwa_index] Pack FASTA... [bns_fasta2bntseq] zero length sequence. Abort!
sh: line 1: 15727 Aborted                 (core dumped) ( /home/share/tool/SOAPfuse-v1.26/source/bin/aln_bin/bwa index /home/share/databases/transcript_index_bwa/transcript.fa )

<Warning>: step transcript_seq_bwa_index failed.
check the command printed, and find what's wrong.

I don't know where it is wrong. Please help!

[iraun]

If you could explain what are trying to do, and present the problem in a clearer way, it would be welcome. It takes up a little more time, but the readers will be grateful for it :).

[syxbestmayer]

SOAPfuse is an open source tool developed for genome-wide detection of fusion transcripts from paired-end RNA-Seq data.

And I want to used it to detect fusion gene.But I meet some difficulties.when I run the my command:

perl SOAPfuse-S00-Generate_SOAPfuse_database.pl \
  -wg /home/share/soapfuse_xsy/hg19.fa \
  -gtf /home/share/soapfuse_xsy/Homo_sapiens.gtf.txt \
  -cbd /home/share/soapfuse_xsy/cytoBand.txt.gz \
  -gf /home/share/soapfuse_xsy/Complete_HGNCGene_Family_dataset.txt \
  -sd /home/share/tool/SOAPfuse-v1.26 \
  -dd /home/share/databases/

<Warning>: step transcript_seq_bwa_index failed.

[iraun]

This file /home/share/databases/transcript_index_bwa/transcript.fa exists and there are sequences inside?

[syxbestmayer]

This file is generated by soapfuse.

[iraun]

So? Can you check if it is there when soap crashes? Also check if /home/share/databases/transcript.fa is there and contains data, because /home/share/databases/transcript_index_bwa/transcript.fa is a link of the first file.

[syxbestmayer]

It contains nothing, I just want to know why

[iraun]

bwa index is complaining because the transcript.fa is empty. You can not do a index of a empty fasta file. Why it is empty? No idea. Have you check if the gtf used is corresponding to the genome file?

[syxbestmayer]

Thank you very much. And how the transcript.fa is generated?

[syxbestmayer]

Can you give a link for ensembl gtf on hg19?