BWA not working with Velvet output

Question

[17501199]

Hello, I am new to bioinformatics and have recently created a de novo assembly in Velvet. I want to align my contigs.fa to the model organism to see the percentage that mapped. I cannot seem to get the script to work correctly.

bwa index -a bwtsw zebrafish_genome.fa.gz
bwa mem -M -t 4 zebrafish_genome.fa.gz* contigs69_1000.fa > bwa_output.sam

Also on a side note? Can I use discosnp to identify variants or is there a better alternative? With discosnp can I use my velvet_asm.afg file?

Thanks

[GenoMax]

What was the output of the index command?

Did you get any errors? What is not working correctly?

[17501199]

From the index I created the 5 output files. amb, ann, bwt, pac and sa. I use the * as I was told all these index files are needed to run bwa mem

[cschu181]

Just for explanation: you need to have all those files (which form the index) present, but the index itself is addressed only by its name, which is the zebrafish_genome.fa.gz.

[cschu181]

Why do you use the * at the end of your index?

[17501199]

it gives me no error but all the options for bwa in the error file and no output

[17501199]

this is what the error file says

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 710 sequences (812701 bp)...
[M::mem_process_seqs] Processed 710 reads in 1.957 CPU sec, 0.492 real sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa mem -t 4 zebrafish_genome.fa.gz contigs.fa
[main] Real time: 15.015 sec; CPU: 3.431 se

[GenoMax]

As @cschu181 said above try running your job like this

bwa mem -M -t 4 zebrafish_genome.fa.gz contigs69_1000.fa > bwa_output.sam

You just need to indicate the basename of the index. In your case that is zebrafish_genome.fa.gz.