Error while running test data

[maojn]

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

[almiheenko]

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

[maojn]

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> >>> . >>> >>

[maojn]

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> >>>> . >>>> >>>

[almiheenko]

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

[minalj365]

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

[Rashadx86]

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

[HLHsieh]

Hi,

I encountered this issue as well.