Error With Soapaligner: Can Not Open Inputfilename
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!
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Ajay A Shettigar •
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joaslucas •
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joaslucas •
2 answers
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.
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Istvan Albert
try providing absolute path in -D MTB.fasta.index like /home/pc/desktop/MTB.fasta.index.
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lakhujanivijay
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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)
I am recently working with Soap and found out that, the aligner expects the proper file names to be mentioned. The input files should end with ".gz" extension and the reference index file should end with ".index" not .fai or any other index file extension. Only then the tool considers the input files and proceeds further with the alignment process.