bowtie can't be found in

[carolynePearl]

hello,

I have created a new environment with the python=2.7 and installed miRge according the instructions. however, when i run the command i get the error "bowtie can't be found in...Please check it." i installed bowtie=1.1.2 and run which bowtie and used the path in my command. however, the error still shows. what would i be doing wrong;

command; (miRge) catugonza@kla-ac-bio-03:~/miRge$ miRge2.0 annotate -s/home/catugonza/miRNA/cbbio-miarma-4c18f6c17c13/ks/raw_reads/iss03.fastq.gz -d miRBase -pb /home/catugonza/miniconda3/envs/miRge/bin/bowtie -lib /home/catugonza/miRge/miRge.Libs -sp human -gff -cpu 1 bowtie can't be found in /home/catugonza/miniconda3/envs/miRge/bin/bowtie. Please check it.

Also tried with; miRge2.0 annotate -s /home/catugonza/miRNA/cbbio-miarma-4c18f6c17c13/ks/raw_reads/iss03.fastq.gz -d miRBase -pb /home/catugonza/miniconda3/envs/miRge/bin/bowtie-1.1.2 -lib /home/catugonza/miRge/miRge.Libs -sp human -cpu 1 bowtie can't be found in /home/catugonza/miniconda3/envs/miRge/bin/bowtie-1.1.2. Please check it.

[arunhpatil]

Hi, thank you for reporting, in order to resolve this, I want to approach this issue in two ways.

• Try the command with -pb /home/catugonza/miniconda3/envs/miRge/bin/
• Can you list the directory contents for /home/catugonza/miniconda3/envs/miRge/bin/bowtie-1.1.2 as in ls -li /path/bowtie-1.1.2.

[carolynePearl]

hello;

1. i tried the command; -pb /home/catugonza/miniconda3/envs/miRge/bin/

Command '-pb' not found, did you mean:

command 'tpb' from deb tpb command 'mpb' from deb mpb

Try: apt install

note; i installed miRge via conda in its own environment .

2. the contents of;/miniconda3/envs/miRge/bin$ less bowtie

   the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

   Bowtie 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. If not, see http://www.gnu.org/licenses/. """

import os import imp import inspect import logging

def main(): logging.basicConfig(level=logging.ERROR, format='%(levelname)s: %(message)s' ) bin_name = "bowtie" bin_s = "bowtie-align-s" bin_l = "bowtie-align-l" idx_ext_l = '.1.ebwtl' idx_ext_s = '.1.ebwt' curr_script = os.path.realpath(inspect.getsourcefile(main)) ex_path = os.path.dirname(curr_script) bin_spec = os.path.join(ex_path,bin_s) bld = imp.load_source('bowtie-build', os.path.join(ex_path, 'bowtie-build')) options,arguments = bld.build_args()

if '--verbose' in options:
    logging.getLogger().setLevel(logging.INFO)

if '--debug' in options:
    bin_spec += '-debug'
    bin_l += '-debug'

if '--large-index' in options:
    bin_spec = os.path.join(ex_path, bin_l)
elif len(arguments) >= 2:
    idx_basename = arguments[-2]
    large_idx_exists = os.path.exists(idx_basename + idx_ext_l)
    small_idx_exists = os.path.exists(idx_basename + idx_ext_s)
    if large_idx_exists and not small_idx_exists:
        logging.info("No small index but a large one is present. Using large index.")
        bin_spec = os.path.join(ex_path,bin_l)

arguments[0] = bin_name
arguments.insert(1, 'basic-0')
arguments.insert(1, '--wrapper')
logging.info('Command: %s %s' %  (bin_spec,' '.join(arguments[1:])))
os.execv(bin_spec, arguments)        

if name == "main": main()

(END)

[carolynePearl]

hello;

sorry i hadn't understood your first instruction;

i used this command; miRge2.0 annotate -s/home/catugonza/miRNA/cbbio-miarma-4c18f6c17c13/ks/raw_reads/iss03.fastq.gz -d miRBase -pb /home/catugonza/miniconda3/envs/miRge/bin/ -lib /home/catugonza/miRge/miRge.Libs -sp human -gff -cpu 1

without specifying the bowtie and it worked perfectly,

thank you a bunch!!!!