Error while running test data #1
Comments
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Hi Jean, Thank you for reporting the issue. Do you have Best regards, |
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Hi Alla,
Do you have a chance to check the error I received? Thank you.
Jean
…On Tue, Feb 25, 2020, 11:32 AM Jean Mao ***@***.***> wrote:
This is the actual error message:
$ /usr/local/apps/tandemtools/tandemquast.py --nano
test_data/simulated_reads.fasta test_data/simulated_polished.fa -o
test_data/simulated_res
2020-02-25 10:18:52 TandemQUAST started
*********************************
Running TandemMapper...
2020-02-25 10:18:53 TandemMapper started
*********************************
K-mers selection started...
Analyzing simulated-polished assembly
Traceback (most recent call last):
File "/usr/local/apps/tandemtools/tandemmapper.py", line 83, in <module>
main()
File
"/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py",
line 764, in __call__
return self.main(*args, **kwargs)
File
"/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py",
line 717, in main
rv = self.invoke(ctx)
File
"/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py",
line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File
"/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py",
line 555, in invoke
return callback(*args, **kwargs)
File "/usr/local/apps/tandemtools/tandemmapper.py", line 74, in main
select_kmers.do(assemblies, raw_reads_fname, reads_fname,
hifi_reads_fname, out_dir, tmp_dir, no_reuse)
File "/usr/local/apps/tandemtools/scripts/select_kmers.py", line 157, in
do
with open(assembly.all_kmers_fname) as f:
FileNotFoundError: [Errno 2] No such file or directory:
'/gpfs/gsfs10/users/apptest4/tandemtools/test_data/simulated_res/simulated-polished_all_kmers.txt'
ERROR: tandemMapper failed! Please check input files and tandemMapper
output. TandemQUAST cannot proceed without alignments
On Tue, Feb 25, 2020 at 11:29 AM Jean Mao ***@***.***> wrote:
> Should I compile flye as well?
>
> On Tue, Feb 25, 2020 at 11:28 AM Jean Mao ***@***.***> wrote:
>
>> It's actually absolute path. I replaced when I edit my message to you.
>> Sorry about that.
>>
>> On Tue, Feb 25, 2020 at 11:12 AM almiheenko ***@***.***>
>> wrote:
>>
>>> Hi Jean,
>>>
>>> Thank you for reporting the issue. Do you have $USER in your error
>>> message or did you replace it before the posting? If the former, it's a bit
>>> weird - could you try to re-run TandemTools using absolute paths instead of
>>> relative ones (e.g., -o /data/user/tandemtools/test_data/simulated_res)?
>>>
>>> Best regards,
>>> Alla
>>>
>>> —
>>> You are receiving this because you authored the thread.
>>> Reply to this email directly, view it on GitHub
>>> <#1?email_source=notifications&email_token=AAG3H62EZDAMK7AOWWI7NUTREU7NPA5CNFSM4K3MFHDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEM4SDUQ#issuecomment-590946770>,
>>> or unsubscribe
>>> <https://github.com/notifications/unsubscribe-auth/AAG3H67NSF3B45HYEBAQBY3REU7NPANCNFSM4K3MFHDA>
>>> .
>>>
>>
|
|
Hi Alla,
Do you have a chance to check the error I received? Thank you. Regards
Jean
…On Wed, Feb 26, 2020 at 5:18 PM Jean Mao ***@***.***> wrote:
Hi Alla,
Do you have a chance to check the error I received? Thank you.
Jean
On Tue, Feb 25, 2020, 11:32 AM Jean Mao ***@***.***> wrote:
> This is the actual error message:
>
> $ /usr/local/apps/tandemtools/tandemquast.py --nano
> test_data/simulated_reads.fasta test_data/simulated_polished.fa -o
> test_data/simulated_res
> 2020-02-25 10:18:52 TandemQUAST started
>
> *********************************
> Running TandemMapper...
> 2020-02-25 10:18:53 TandemMapper started
>
> *********************************
> K-mers selection started...
>
> Analyzing simulated-polished assembly
> Traceback (most recent call last):
> File "/usr/local/apps/tandemtools/tandemmapper.py", line 83, in <module>
> main()
> File
> "/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py",
> line 764, in __call__
> return self.main(*args, **kwargs)
> File
> "/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py",
> line 717, in main
> rv = self.invoke(ctx)
> File
> "/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py",
> line 956, in invoke
> return ctx.invoke(self.callback, **ctx.params)
> File
> "/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py",
> line 555, in invoke
> return callback(*args, **kwargs)
> File "/usr/local/apps/tandemtools/tandemmapper.py", line 74, in main
> select_kmers.do(assemblies, raw_reads_fname, reads_fname,
> hifi_reads_fname, out_dir, tmp_dir, no_reuse)
> File "/usr/local/apps/tandemtools/scripts/select_kmers.py", line 157,
> in do
> with open(assembly.all_kmers_fname) as f:
> FileNotFoundError: [Errno 2] No such file or directory:
> '/gpfs/gsfs10/users/apptest4/tandemtools/test_data/simulated_res/simulated-polished_all_kmers.txt'
> ERROR: tandemMapper failed! Please check input files and tandemMapper
> output. TandemQUAST cannot proceed without alignments
>
> On Tue, Feb 25, 2020 at 11:29 AM Jean Mao ***@***.***> wrote:
>
>> Should I compile flye as well?
>>
>> On Tue, Feb 25, 2020 at 11:28 AM Jean Mao ***@***.***> wrote:
>>
>>> It's actually absolute path. I replaced when I edit my message to you.
>>> Sorry about that.
>>>
>>> On Tue, Feb 25, 2020 at 11:12 AM almiheenko ***@***.***>
>>> wrote:
>>>
>>>> Hi Jean,
>>>>
>>>> Thank you for reporting the issue. Do you have $USER in your error
>>>> message or did you replace it before the posting? If the former, it's a bit
>>>> weird - could you try to re-run TandemTools using absolute paths instead of
>>>> relative ones (e.g., -o /data/user/tandemtools/test_data/simulated_res)?
>>>>
>>>> Best regards,
>>>> Alla
>>>>
>>>> —
>>>> You are receiving this because you authored the thread.
>>>> Reply to this email directly, view it on GitHub
>>>> <#1?email_source=notifications&email_token=AAG3H62EZDAMK7AOWWI7NUTREU7NPA5CNFSM4K3MFHDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEM4SDUQ#issuecomment-590946770>,
>>>> or unsubscribe
>>>> <https://github.com/notifications/unsubscribe-auth/AAG3H67NSF3B45HYEBAQBY3REU7NPANCNFSM4K3MFHDA>
>>>> .
>>>>
>>>
|
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Hi Jean, Sorry for the delay! I suspect that the error can be related to Jellyfish. I changed TandemTools to use the installed version of Jellyfish instead of compiling it. Could you please try to update TandemTools and re-install it? I added regex and jellyfish to conda requirements - thank you for reporting these issues. Alla |
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Hi There, I just installed Tandemtools and ran the same command as Jean and got the same error, along with jellyfish error: 2020-11-12 17:10:36 TandemQUAST started Running TandemMapper... K-mers selection started... Could you please look into this? Thanks, |
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Hi all, Installing jellyfish from conda didn't seem to install the binary, just the python modules. Installing Jellyfish from source (and adding the resulting bin directory to the path) resolved this error: https://github.com/gmarcais/Jellyfish Thanks, |
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Hi, I encountered this issue as well. |
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Hi,
Thank you for offering tandemtools.
I have installed tandemtools :
conda install --file requirement.txt
and also installed regex and compiled jellyfish after receiving errors (not in installation instruction).
Then I got the following error:
$ /usr/local/apps/tandemtools/tandemquast.py --nano test_data/simulated_reads.fasta test_data/simulated_polished.fa -o test_data/simulated_res
2020-02-25 10:18:52 TandemQUAST started
Running TandemMapper...
2020-02-25 10:18:53 TandemMapper started
K-mers selection started...
Analyzing simulated-polished assembly
Traceback (most recent call last):
File "/usr/local/apps/tandemtools/tandemmapper.py", line 83, in
main()
File "/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/Anaconda/envs_app/tandemtools/current/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/usr/local/apps/tandemtools/tandemmapper.py", line 74, in main
select_kmers.do(assemblies, raw_reads_fname, reads_fname, hifi_reads_fname, out_dir, tmp_dir, no_reuse)
File "/usr/local/apps/tandemtools/scripts/select_kmers.py", line 157, in do
with open(assembly.all_kmers_fname) as f:
FileNotFoundError: [Errno 2] No such file or directory: '/data/$USER/tandemtools/test_data/simulated_res/simulated-polished_all_kmers.txt'
ERROR: tandemMapper failed! Please check input files and tandemMapper output. TandemQUAST cannot proceed without alignments.
Did I miss anything during installation? Thank you for your help.
Regards,
Jean
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