Hey,
I'm trying to preform a bisulfite alignment using gmapR package. This is my code:
=========================
library("gmapR")
ggd<-GmapGenomeDirectory(file.path(getwd(),"indices"), create=T)
gg<-GmapGenome(file.path(getwd(),"test.fa"), directory=ggd, name="seq", create=T)
cmet_index <- cmetindex(gg)
gsnapPar <- GsnapParam(genome=gg, unique_only=FALSE, suboptimal_levels=2L, npaths=1000L, novelsplicing=FALSE,clip_overlap=FALSE, mode="cmet-stranded")
gsnapOutput<- gsnap(input_a="/primers/Fprimers.fasta",input_b="/primers/Rprimers.fasta", params=gsnapPar, output = "primer.out")
================================
Everything is going well until starting the alignment using gsnap function so I am getting the follwoing error:
######
Error in .system_gsnap(commandLine("gsnap")) :
Execution of gsnap failed, command-line: /lib/R/library/gmapR/usr/bin/gsnap --db=seq --dir=/indices --suboptimal-levels=2 --mode=cmet-stranded --npaths=1000 --format=sam --split-output=primer.out /primers/Fprimers.fasta primers/Rprimers.fasta 2> /tmp/RtmpmHpuzf/gsnap-stderr2e90db57601log'; last output line: 'Cannot find genomic index files in either current or old format'
######
Any advice?
Thanks in advance!
Best,
Amer
If you look in
/indices, do you see aseqdirectory with files in it? I'm guessing something is just getting confused about the paths.yes inside indices directory i have seq directory and it includes the following files:
seq.maps (empty directory)
seq.chromosome
seq.chromosome.iit
seq.chrsubset
seq.contig
seq.contig.iit
seq.genomebits
seq.genomecomp
seq.ref153positions
seq.ref12153bitpackcomp
seq.ref12153bitpackptrs
seq.ref12153gammaptrs
seq.ref12153offsetscomp
seq.saindex
seq.salcpcomp
seq.salcpptrs
seq.sarray
seq.version
=====
beside seq directory, indices directory includes the following files as well:
seq.metct153positions
seq.metct12153bitpackcomp
seq.metct12153bitpackptrs
seq.metga153positions
seq.metga12153bitpackcomp
seq.metga12153bitpackptrs
I found someone had the same problem but with no clear way how he solved it:
http://seqanswers.com/forums/archive/index.php/t-58056.html
Are you able to provide something reproducible?
it's not the elegant way but let's try with it (or by email?)
Fprimers.fasta:
>1
ggtggaattttgtgttagttttgggt
===============
Rprimers.fasta:
>1
aactttccacctaactactaccctta
===========
test.fa (RefGenome):
>seqasdf
AGACAAAACAGAAAACTTTATGGAAGATAAAATAAGAATAACAAAATCTTTCCCAAAGAGAAAGACCATTAAATTTTTGT
ATATATCCTTCCAGAGAATACACAAATTATATGTATATATATTTTACATGTATACATATATAACAAAGACTAGCTTATAC
TACCCACGCTTTCCTGTCATTTTTCTTTTCTACCTAAGATATCACTGACAGTCTTTTATATAATAAGGATAGTCCTCAAT
TATCATCATTGTTTAAATGGAATTCTAATGTGTTAAGTGCCATAAATTAGCAGATTCTCTATTGATAGACATTTAGCTTA
CTTTTCACATTCTCACTATGAGTAATGCTAAGAAGGCAATATAGTTCTTGCACCTTCATGAACATATTCTTTTATGCTAT
GTGCATTATTTTGGGTCAAAGGGCAAGCAGAGTTTCATTTAATTTTGTTTTAGACATGGGCTATATATTGACAAATTGCC
CTCCCAGGAACAGTACACAGTTTTTCTTATGTTGCCTCACCCATGCCAGCAGTAGCTAGAAAATGCATTTCCAAAGACTG
GTGCTAATTTTCTGTGCATTCTGTGAGTGCTCAGTCAATTTAAGCAATAACCACTTAGAGTAACAAAATCTATTCACCCT
AATAGCAGAGATTTCTACTTCATCCCTGGCTCACTGCCCAACTTTTGATCTCATCTAAGGCCAATAAATGTAGCTCCAGA
CAAGTGACACAGGTAGCTCTGTCCCCATCCAATCTACCCAGCTACTTCTCTTAAGGCACGTTCTGATCCTTCAAGCATGA
AGTTCTTGCCTCTGGCTTTTGTTTCTCTCTTGTTTCTGGCTTCAGTGACCTTGAGTACCCTGGAATCTTCCATATTGAGA
AAGAAATGATAGAGGGGAGGGGACATGGAAAAAAGAATTAAATATATCTATTTTTAAAAAGAAAGAAAATTTTAGAATGG
ACATGTCTAGAAGGAGGAGGAAACAGAGGAGGGGGACAGGTATAAAAACTGGACTTCTCTGAATATACTCTGCTTTGAAG
GTTTGACTTTGGAATCATCTACATATTTTATCTAATACAAGAATATCGAAACTTAAATGGCAATCCCAAAAATCTAAAAG
GAATAGAAATCAAATTAGCCTCTGTAATAAATGGGTTGTATAACCACACAAAGGACTATTTGAAATGACTTTCAAAGAGT
AATTTGAGAATACTTCCTTATTGGAATATAACCTAAAAACAGAAGAATTGCAAACTGTTTTCAATGTTTTCAGTAATCAT
ATTGAGACTTTAATACATATATTGTGGGATAAAGGAAATGAATGTTGGTGTCACTGATAGAGATAAGAAATAAAAGTTCA
GGTAAAAATTCTGTAAATCCTAAATTTGAATTGGAATTTTATATTTTATTTTTAAAATACCTTTTTCTACCCCCATCCAC
TGAAAAGCCCTAGAAATATTGGCCAACCTAGTAGAAATGATTTCCCTCTCACCCGGGATATTATCTCTAAATATAATTTA
CCAAAGTCTTATTGAAGAAATTGCTGTTTCTGAGCTTGAAGCAACTATACAAATGTACCTGGAAGATTTTACCATACTGG
AAAAAAGCAGCTTGACAAAGACTACTGAAGTCATGTCAAAAAAAACAAAGAAGTCAACTTGAAGGGGCTTTCTCTTGGCA
AAGATGGGAAAATGTGAACCTTGATAAAAAATAATTGCATGCATTATTCACAGTAACCAAGATATGTAATCCACCTAGGT
GTCTATGGATGGATAAATATATAAAGAAAATGTGATATACACAATGAAATATTATTCAGCCTTTAAAAAGAAAGAAATCC
TGCCATTTGTGACAACACAGATGAACCTGGAGGACATTATGCTAAGTGAAATAAGCCAGACACAGGCAGACAAATACTGA
ATGATCTCACCTATGTGTGGAATCTTAAAATGTCAAACTCATGGACACAGAGAGTAGGATGGTGGTTACCAAGGGAGTTG
AGGGAAATGAAGAAGTACTAGTCAAAGGGTACAAAGTTTCCGTTATGCAGGGTGAATAAGTTCGGGAGCTTACTGCATAG
CACAGTGACTACAGTTAATAATACTGTGTTGTATACTTGAAATTTGCTAAGAGTAGATCTTAAATATTGTTACCACAGAA
AAAAATGGTGACTATGAGAGGTGATGAATATGTTAATTAGCTTGATAGTGGTAATCATGTCACAATGTATATGTCTATCA
AAACATCACATTGTACGTCTTAAATATGTACAATTATTATTTGTCAATTATACCTCAATAAAGCTGGAAACATAAAAATA
AAATAACTACAATTAATTGAAACATATCAAACATGTCCAAAACTGATAAAGAAAGGTAAAGAATTTGGCCTGGCACAGCG
GCTCACACCTGCAATCTCAGCAGTTTGGGATGCCAAGGCAGGCGGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGC
CAATATAGCAAAACCCCATCTCTACTAAAAATACAAAAATTAGCTAGGCGTGGTAGCGGGCATCTGTAGTTCCAGCTACT
ACTCAGGAGGCTGAGATAGAGAATCACTTGAACCCAGAGGTGGAGGTTGCAGTGAGCCGAGATCACGCCACTATACTCCA
GCCTGGGTGACAAAGTGAGACTCTGTCTCAAAAAAAAAAAAAAAAGAAAGAAAGAAAAGTGAAGAATTTATCCTGGCTTT
TCTGTAAAAACTGCACCTCAGAAGAACCAAATTATTGATAAGGAATTTTGCTCTTTAGAAATATTTCCAGCTAATAAATG
AAGGAATAATAGCATTGAGACAAATCGCCATTTTGTAATCTCAGGTGAATTTACGGATCTAGGCAATGATCATTAATGGC
TGAGAAAATCACAACAAAAAGAACAATTAGACATTTGTGCCTCCTGATAGAAGTATACAATATCACCTTCAAAGCTATTT
TGCCAAAAAAGAAAAAAAAAATCAACCCAAATCTAATCAAGGCTCCCACTCTAACTCCCAAGCTCTAGGATATACCAAGG
ACAAAGGAAGATCATGAAATACCACCATGGGGATTCAATCAGCAAATTCTGAAATGCAACATTATCCTTCACCCTGCTTG
GCCTAAAAGTACAAAATAACACGAGGAAAAATTAGTTTCCAGAGCCTGTTATATTTTGAAAAATCATCAGAAAACTGAGA
ATCAAGGATAGAATTTCTAGAAAGTTCCTTCCCCTAAAGCTTTCACACTTGCCTCAGTGTATATATGTGGCTATACCACT
GACAGGCCGCCAGTCATTAAATTCAAGCTCCAAGAGACAAACTCTTGAAAAAAAGGCAGCCTAGGAGAAAGCAACATGAT
TTTTCACATATTTTAACTTGGTTTTTCTCATAAAATGGTTTCTGAATGTTTCTTAGCTTTCAATGGGCAATAAATAACTT
TTAGGGAAATAGATGTGAGCCAATCTGAGGAAGTATTTGAGATGAAGAGAAGGCTTTGCTGTCTATGAGGAGTGCATTAG
AATAGAATCGCTCCAGGAAAAGGTCACCTGTGTTGATTGCCTTTATGAGGTGACATTTAAATAAAAGTACTCGTTCAGTT
TTCATTGAAAAACATTAAAAGACATCTCCAAAAATTTTTTTGGGAATGTGAGAAACTCTGCTGCACAAATGATCATGTTT