TandemTools
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ablab
Error while running test data
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
Did I miss anything during installation? Thank you for your help.
Regards,
Jean
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
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 [email protected] 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
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 [email protected] wrote:
Should I compile flye as well?
On Tue, Feb 25, 2020 at 11:28 AM Jean Mao [email protected] 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 [email protected] 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 https://github.com/ablab/TandemTools/issues/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 [email protected] 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 [email protected] 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
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 [email protected] wrote:
Should I compile flye as well?
On Tue, Feb 25, 2020 at 11:28 AM Jean Mao [email protected] 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 [email protected] 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 https://github.com/ablab/TandemTools/issues/1?email_source=notifications&email_token=AAG3H62EZDAMK7AOWWI7NUTREU7NPA5CNFSM4K3MFHDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEM4SDUQ#issuecomment-590946770, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAG3H67NSF3B45HYEBAQBY3REU7NPANCNFSM4K3MFHDA .
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
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... 2020-11-12 17:10:37 TandemMapper started
K-mers selection started... Jellyfish is not found in your PATH! Please install Jellyfish and rerun TandemTools. Jellyfish can be installed through conda install jellyfish ERROR: tandemMapper failed! Please check input files and tandemMapper output. TandemQUAST cannot proceed without alignments
Could you please look into this?
Thanks, Minal
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, Rashad
