Question: Bowtie run error
0
gravatar for mikemwanga6
2.1 years ago by
mikemwanga60 wrote:

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.

assembly • 849 views
ADD COMMENTlink modified 2.1 years ago by genomax68k • written 2.1 years ago by mikemwanga60

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.

ADD REPLYlink written 2.1 years ago by Sej Modha4.2k

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

ADD REPLYlink written 17 months ago by freuv20
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