mapper.pl doesn't find bowtie index when given index name is wrong

[lizhan96]

hi there,

when i run the following code, i got this error message.

$mapper.pl /data_6t/lizhan/01.project/nanfangyi/miRNA/data/N154_clean_total.fa -c -i -j -l 18 -m -p /data_6t/lizhan/database/reference/ucsc.hg19.fa -s N154_reads_collapsed.fa -t N154_reads_vs_refdb.arf -v -o 4

converting rna to dna alphabet discarding sequences with non-canonical letters discarding short reads collapsing reads mapping reads to genome index Could not locate a Bowtie index corresponding to basename "/data_6t/lizhan/database/reference/ucsc.hg19.fa" Please make sure you used bowtie version 1 to build the index. Usual index files have suffix .ebwt

the ucsc.hg.19.fa index i got from the following code /data_6t/lizhan/02.software/bowtie/bowtie-1.3.1-linux-x86_64/bowtie-build ucsc.hg19.fasta ucsc.hg19.fasta

there's no any error message.

would you help me solving the error? Thanks!!

[Drmirdeep]

Please check if the bowtie files are all present at directory /data_6t/lizhan/database/reference/

[lizhan96]

$l /data_6t/lizhan/database/reference/ucsc.hg19.fasta* -rw-r--r-- 1 lizhan ubuntu 3.0G Jun 21 15:13 /data_6t/lizhan/database/reference/ucsc.hg19.fasta -rw-r--r-- 1 lizhan ubuntu 794M Jun 21 15:11 /data_6t/lizhan/database/reference/ucsc.hg19.fasta.1.ebwt -rw-r--r-- 1 lizhan ubuntu 346M Jun 21 15:11 /data_6t/lizhan/database/reference/ucsc.hg19.fasta.2.ebwt -rw-r--r-- 1 lizhan ubuntu 4.8K Jun 21 13:51 /data_6t/lizhan/database/reference/ucsc.hg19.fasta.3.ebwt -rw-r--r-- 1 lizhan ubuntu 691M Jun 21 13:51 /data_6t/lizhan/database/reference/ucsc.hg19.fasta.4.ebwt -rw-r--r-- 1 lizhan ubuntu 794M Jun 21 16:32 /data_6t/lizhan/database/reference/ucsc.hg19.fasta.rev.1.ebwt -rw-r--r-- 1 lizhan ubuntu 346M Jun 21 16:32 /data_6t/lizhan/database/reference/ucsc.hg19.fasta.rev.2.ebwt

I believe that it's already complete.

[Drmirdeep]

/data_6t/lizhan/database/reference/ucsc.hg19.fasta != /data_6t/lizhan/database/reference/ucsc.hg19.fa