Error With Soapaligner: Can Not Open Inputfilename

Question

[joaslucas]

I have got something that seems to be a simple problem running SOAPaligner but, unfortunatelly I still could not solve it. After using the commands bellow, the SOAP simply respond "Cannot open input file. I woul be glad if someone give me a help. Thanks

[root@joas Documentos]# /home/joas/Documentos/soap2.21release/soap -D MTB.fasta.index -a /home/joas/Documentos/read_a/B4.fastq -o /home/joas/Documentos/soap2.21release/read_out -u unmapped

Begin Program SOAPaligner/soap2
Tue Feb 19 23:21:56 2013
Reference: MTB.fasta.index
Query File a: /home/joas/Documentos/read_a/B4.fastq
Output File: /home/joas/Documentos/soap2.21release/read_out
             unmapped
Load Index Table ...
DNALoadPacked() : Cannot open inputFileName!

[Michael]

The input file doesn't exist: typo reada/reads? Moderators, please leave a comment when closing, even if you think the reason is obvious (e.g. not a bioinformatics question - typos when using a bioinformatics program are not a bioinformatics problem)

Answer 1

[Istvan Albert]

As Michael Dondrup says make sure that all input files exists.

What is really important however is to stop running tools as root user. Pain and suffering lies that way.

Answer 2

[lakhujanivijay]

try providing absolute path in -D MTB.fasta.index like /home/pc/desktop/MTB.fasta.index.