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  • Problem with Bowtie 2

    Hi, I am a student and I'm doing work with data obtained by ChiPSeq. I am trying to do the alignment of the reads with the reference genome, but I get the following error:

    system("./bowtie2-build ./data/tair10.fasta ./data/tair10.fasta") # Indexes reference genome

    ./bowtie2-build: 20: ./bowtie2-build:
    Copyright 2014, Ben Langmead <[email protected]>

    This file is part of Bowtie 2.

    Bowtie 2 is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    Bowtie 2 is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
    : not found
    from: can't read /var/mail/collections
    ./bowtie2-build: 31: ./bowtie2-build: Syntax error: "(" unexpected

    Then, I attempt to put in place the following commands and I get this error:

    > resources <- list(walltime="1:00:00", ntasks=1, ncpus=cores(args), memory="10G")
    > reg <- clusterRun(args, conffile=".BatchJobs.R", template="slurm.tmpl", Njobs=18, runid="01",
    + resourceList=resources)

    Creating dir: /home/usuario/chipseq/results/submitargs01_BJdb_7642
    Saving registry: /home/usuario/chipseq/results/submitargs01_BJdb_7642/registry.RData
    Adding 18 jobs to DB.
    Error in system2(command = command, args = args, stdout = stdout, stderr = stderr, :
    error in running command
    Además: There were 40 warnings (use warnings() to see them)

    > waitForJobs(reg)
    Error in checkRegistry(reg, writeable = FALSE) :
    objeto 'reg' no encontrado

    I don't know where can be the problem. I'm using the tutarial of the following web http://girke.bioinformatics.ucr.edu/...hIPseq_04.html
    for ChIPSeq Analysys. I am working on RStudio with the package systemPipeR

  • #2
    For reference cross-posted: https://www.biostars.org/p/301685/#306693

    Comment

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