Error in running Bowtie2 #24
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Hello Guy, Traceback (most recent call last): File "rnalysis\utils\io.py", line 1479, in generate_base_call File "rnalysis\utils\io.py", line 1420, in run_subprocess File "subprocess.py", line 858, in init File "subprocess.py", line 1311, in _execute_child FileNotFoundError: [WinError 2] The system cannot find the file specified During handling of the above exception, another exception occurred: Traceback (most recent call last): File "rnalysis\gui\gui.py", line 3697, in finish_generic_job File "rnalysis\gui\gui_widgets.py", line 329, in run File "rnalysis\fastq.py", line 747, in bowtie2_align_paired_end File "rnalysis\fastq.py", line 803, in _parse_bowtie2_misc_args File "rnalysis\utils\io.py", line 1482, in generate_base_call FileNotFoundError: RNAlysis could not find 'bowtie2'. Please ensure that your installation folder is correct, or add it to PATH. I have been trying to figure out this from the past two days. Still I didn't find any solution. Can you please help me with this?
Thank you |
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Replies: 9 comments
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Hello Guy, |
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Hi, |
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I didn't set any I went with the default.
…On Thu, May 25, 2023, 4:27 PM Guy Teichman ***@***.***> wrote:
Hi,
What is the value you set for the parameter "bowtie2_installation_folder"?
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Hello Guy,
Good noon,
Can you please guide me what parameters am I suppose to set ??
On Thu, May 25, 2023, 4:54 PM rajarajeshwari rajkumar <
***@***.***> wrote:
… I didn't set any I went with the default.
On Thu, May 25, 2023, 4:27 PM Guy Teichman ***@***.***>
wrote:
> Hi,
> What is the value you set for the parameter "bowtie2_installation_folder"?
>
> —
> Reply to this email directly, view it on GitHub
> <#23 (comment)>,
> or unsubscribe
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The parameters now is
@echo off
perl %~dp0/bowtie2 %*
On Fri, May 26, 2023, 12:05 PM rajarajeshwari rajkumar <
***@***.***> wrote:
… Hello Guy,
Good noon,
Can you please guide me what parameters am I suppose to set ??
On Thu, May 25, 2023, 4:54 PM rajarajeshwari rajkumar <
***@***.***> wrote:
> I didn't set any I went with the default.
>
> On Thu, May 25, 2023, 4:27 PM Guy Teichman ***@***.***>
> wrote:
>
>> Hi,
>> What is the value you set for the parameter
>> "bowtie2_installation_folder"?
>>
>> —
>> Reply to this email directly, view it on GitHub
>> <#23 (comment)>,
>> or unsubscribe
>> <https://github.com/notifications/unsubscribe-auth/A6TURHLUIZL4OL4HVQ3T4O3XH43KBANCNFSM6AAAAAAYM3ZY6M>
>> .
>> You are receiving this because you authored the thread.Message ID:
>> ***@***.***>
>>
>
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Hi, |
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Hello Guy,
I'm really sorry to bother you a lot. But I'm not sure which is
installation folder.
…On Fri, May 26, 2023, 10:21 PM Guy Teichman ***@***.***> wrote:
Hi,
please try setting the 'bowtie2_installation_folder' to point to the
folder in which you installed bowtie2.
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Hello Guy,
Can you please guide me with this step by step??
Thank you
On Sat, May 27, 2023, 12:54 PM rajarajeshwari rajkumar <
***@***.***> wrote:
… Hello Guy,
I'm really sorry to bother you a lot. But I'm not sure which is
installation folder.
On Fri, May 26, 2023, 10:21 PM Guy Teichman ***@***.***>
wrote:
> Hi,
> please try setting the 'bowtie2_installation_folder' to point to the
> folder in which you installed bowtie2.
>
> —
> Reply to this email directly, view it on GitHub
> <#23 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/A6TURHPGOZITR5L5MIWIBDTXIDNQBANCNFSM6AAAAAAYM3ZY6M>
> .
> You are receiving this because you authored the thread.Message ID:
> ***@***.***>
>
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You have downloaded and installed the tool 'bowtie2'. You installed it at a specific location on your computer - this is the "installation folder". |
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You have downloaded and installed the tool 'bowtie2'. You installed it at a specific location on your computer - this is the "installation folder".
You should set the 'bowtie2_installation_folder' parameter in RNAlysis, so it points to the folder in which you installed bowtie2.