I am running bowtie (1) and the tool doesnt seem to recognize the indexes (although they are present in the directory, I have specified). Any clues?
ubuntu@ip-172-31-15-51:~$ ./rung
Could not locate a Bowtie index corresponding to basename "/home/ubuntu/bowtie-indexes/mm9"
Command: /home/ubuntu/bowtie-master/bowtie-master/bowtie -m 1 -p 6 -S /home/ubuntu/bowtie-indexes/mm9 fastq/myc.fastq.gz myc.sam
ubuntu@ip-172-31-15-51:~$ ls bowtie-indexes/mm9
chr10.fa chr13.fa chr16.fa chr19.fa chr3.fa chr6.fa chr9.fa chrY.fa mm9.2.ebwt mm9.ebwt.zip mm9.rev.2.ebwt
chr11.fa chr14.fa chr17.fa chr1.fa chr4.fa chr7.fa chrM.fa make_mm9.sh mm9.3.ebwt mm9.fa
chr12.fa chr15.fa chr18.fa chr2.fa chr5.fa chr8.fa chrX.fa mm9.1.ebwt mm9.4.ebwt mm9.rev.1.ebwt
ubuntu@ip-172-31-15-51:~$ ./rung
Could not locate a Bowtie index corresponding to basename "/home/ubuntu/bowtie-indexes/mm9"
Command: /home/ubuntu/bowtie-master/bowtie-master/bowtie -m 1 -p 6 -S /home/ubuntu/bowtie-indexes/mm9 fastq/myc.fastq.gz myc.sam
ubuntu@ip-172-31-15-51:~$ ls bowtie-indexes/mm9
chr10.fa chr13.fa chr16.fa chr19.fa chr3.fa chr6.fa chr9.fa chrY.fa mm9.2.ebwt mm9.ebwt.zip mm9.rev.2.ebwt
chr11.fa chr14.fa chr17.fa chr1.fa chr4.fa chr7.fa chrM.fa make_mm9.sh mm9.3.ebwt mm9.fa
chr12.fa chr15.fa chr18.fa chr2.fa chr5.fa chr8.fa chrX.fa mm9.1.ebwt mm9.4.ebwt mm9.rev.1.ebwt
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