Bowtie run error

Question

[mikemwanga6]

I am running SSPACE after assembly of reads using SPADES. However SSPACE returns the following error.

command:

perl ~/my_scripts/SSPACE/SSPACE_Basic.pl -l libraries.txt -s contigs.fasta -k 5 -a 0.7 -x 0  -b standard_out

Error:

Your inserted inputs on [SSPACE_Basic v2.1] at Mon May 15 13:10:55 2017:
Required inputs: 
    -l = libraries.txt
    -s = contigs.fasta
    -b = standard_out

Optional inputs:
    -x = 0
    -z = 0
    -k = 5
    -a = 0.7
    -n = 15
    -T = 1
    -p = 0


=>Mon May 15 13:10:55 2017: Reading, filtering and converting input sequences of library file initiated
Reading read-pairs lib1.1 @ 0       

------------------------------------------------------------

=>Mon May 15 13:10:56 2017: Storing contigs to format for scaffolding

LIBRARY lib1
------------------------------------------------------------

=>Mon May 15 13:10:56 2017: Reading contig file

=>Mon May 15 13:10:56 2017: Building Bowtie index for contigs

**Bowtie-build error; -1 at /home/local/KWTRP/mmwanga/my_scripts/SSPACE/bin/PairingAndScaffolding.pl line 823.**

Your help will be valuable.

[Sej Modha]

I have always had issue with running bowtie within SSPACE so I have used bwa instead. You can try bwa if you have bwa available in the path.

[freuv]

How do you switch from Bowtie to BWA on SSPACE v2?