So what seems to be a super-easy problem has proved itself difficult to resolve. I've posted the the SOAP mailing list and to the contact email listed on the SOAP website...
Basically, I get this an error that seems to refer to the input fasta file..
The command:
The painful results:
Here are the reads:
The error seems so elementary, yet, I have been unable to solve. The reads seems to be fine, and permissions are set appropriately.
Anybody know how to fix this problem?
Basically, I get this an error that seems to refer to the input fasta file..
The command:
Code:
macmanes@macmanes:~/soap-2.20$ ./soap -D /home/macmanes/soap-2.20/ tuco.fa.index –a /home/macmanes/soap-2.20/reads_a.fa -o /media/hd/tuco/mrna/ SOAP_results/soap
The painful results:
Code:
Begin Program SOAPaligner/soap2 Fri Apr 16 12:51:34 2010 Reference: /home/macmanes/soap-2.20/tuco.fa.index Query File Error: Can't read
Code:
macmanes@macmanes:~/soap-2.20$ head /home/macmanes/soap-2.20/reads_a.fa >1 CAGATATCTTGGGGAGCTCCGGGCGTAGCAGGGTTGGGGAGCCGTGAGAGGGGGCGGCTGTCAGGGCCGGGTGGCACCGGGCGGGCGCGCGCCCGCCTGCCT >2 CGGGAAGCGGGGAGCCTGAAGCTGGGGCCACCCCTCGCCGCCACCGGCGTGCAGCCGCCCAGGATTGCAGCCCGGAAGGGTCCCCCTGCAGGGGGTCTGGCG >3 GTTCCATGTGAACAGCAGTTGAACATGGGTCAGTCGGTCCTGAGAGATGGGCGAGCGCCGTTCCGACGGGACGGGACGACGGCCTCCGTCGCCCTCAGCCGC >4 TGGGTCCCCATTAGAGGCGGTGAAATCGATGGCCACCGTGAAGCTGGTCTGGCAGCCGCCCCTGATGTAACCCAGAGACGGTGTGCACCTTTTCCACCGCGC >5 GCCAGCCTGAACAACATCATGAGACTTTGTCTTGGGAGGCAAAAAGAGAAACTTAGACTATTCACATTAGAAATCAAGTAACAGAAACAACATCTCCATTCA
Anybody know how to fix this problem?
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