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Old 03-29-2018, 01:12 PM   #1
Junior Member
Location: Murcia, Spain

Join Date: Mar 2018
Posts: 1
Default 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 <>

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
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 <>.
: 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
for ChIPSeq Analysys. I am working on RStudio with the package systemPipeR
eduillueca is offline   Reply With Quote
Old 03-29-2018, 05:37 PM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,825

For reference cross-posted:
GenoMax is offline   Reply With Quote

bowtie 2, chip seq

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