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problems running constax #3
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Hi ramiroricardo, There are two things that I have noticed might need to be fixed:
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Hi @liberjul , Thanks for your quick reply. When I run the same code, but with the
About your 2nd question, none of the tools were working outside of the environment. Though I note that I was running this not as a bash script, but directly on terminal. I had previously ran it inside a bash script, also with the same errors, while adding the following before calling constax:
Inside the environment, all tools appeared to be working as these produced the expected output when calling
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Hello @ramiroricardo, Can you please post what you have in your pathfile.txt? Also, it should be placed in your working directory not in the conda environment. See details https://constax.readthedocs.io/en/latest/tutorial1.html |
Hi @Gian77 , Thanks for your reply. My path file, that was in the conda environment folders, has the following:
Note that I did not do any modification to this, it came when I created the conda environment. If I create a pathfile in the working directory as:
and run:
I get this:
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Beside you have `--make-plot' twice in your script. Do you have vsearch in the same conda environment? Please post
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hi @Gian77 , Thanks for pointing out the error with Here are the outputs of the commands that you asked for:
Thanks again for your help |
Hi @ramiroricardo, It appears that the environment is not activated when subscripts were called, so I updated the If you rerun constax after replacing this script, does it work? Please show the output if not. Julian |
Hi all, Sorry that I have not replied in a while, but only managed to get back to this now. I reinstalled constax with conda and am now using constax version 2.0.13. I have also tried to replace the constax_wrapper.py, but irrespectively of whether I keep the constax_wrapper.py file installed with conda or use this one, I get the same result. So when I run:
I get the errors
If you have any idea on what could be leading to this, I would like to keep trying to solve it. |
Hi all, I have tried to run the same code in a different virtual machine and now it does seem to run. Not sure what was the problem in the other VM. However, I am getting an error at the end. I am not sure, but it seems to me that constax is running twice, which might be leading to that final error. So I ran:
and got:
Also, in the tutorial, you show a consensus_taxonomy.txt file, which I don't see in my results. Was this replaced by the constax_taxonomy.txt output? Best, |
Hi Ramiro, I am currently working on a fix to some of the pathfile issues which seem to be present. Also, I need to update the tutorial to reflect that we changed It probably ran twice because an error was detected, but this error was overcome in the script. I will work to make the double run not occur in that case. Thank you again for the feedback, and I will be posted another update shortly so you can run yours on a local machine. Julian |
It appears that running twice was not caused by the RDP duplicate taxa error, but instead something else. Could you upload the contents of the log file found in your working directory? It should be named I'll also look into the error in the plotting script. |
Hi Julian, I was just testing and the --make_plot option appears to be the culprit for this to run twice. If I run constax without it, it runs once with no errors. I am attaching two log files run with and without this option. The latest one is without the option. log_constax2_2021-06-24_17-27-05.txt |
Thanks for sending those. I fixed the Rscript (new one below), and will push a new version once I get these path issues worked out.
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Hi, I have similar issue but my log file has a bit different error messages, namely: /opt/anaconda3/envs/CONSTAX/opt/constax-2.0.15-0/constax_no_inputs.sh: line 127: blastn: command not found rm: : No such file or directory It is odd because outside of constax it is possible to run all of the mentioned modules. This is the command I used: And this is what the Terminal prints out: Overwritting previous classification... Assigning taxonomy to OTU's representative sequences Combining Taxonomies In the end, there are empty blast files in the taxonomy_assignements folder. So I guess the issue relates to my Apple M1 chip(?) Any solution to this? |
Hi @mtva0001, |
Hi @mtva0001, |
Thanks a lot for your quick help! I did as you suggested, there is a difference this time but still not running properly: Command I ran: The log file: Reading file ./training_files//sh_general_release_dynamic_10.05.2021__UTAX.fasta 100% Reading UDB file ./training_files//sintax.db 100% Fatal error: Unable to open file for reading () rm: : No such file or directory |
Hi @mtva0001, I pushed new versions of the Also, it would be helpful to see the packages installed both inside and outside of your CONSTAX environment. You can print these with |
Hi! Thanks again for your quick response! vsearch v2.16.0_macos_x86_64, 16.0GB RAM, 8 cores Reading file ./training_files//sh_general_release_dynamic_10.05.2021__UTAX.fasta 100% Reading UDB file ./training_files//sintax.db 100% Fatal error: Unable to open file for reading () rm: : No such file or directory Conda lists: |
Hello @mtva0001, |
Hi, Sorry for the late reply. I just tried it but it gives me the same error: rm: : No such file or directory |
Dear all, I have a similar issue. I was running: constax And here is the error from the log file: I will greatly appreciate some help! Thank you in advance. |
HI @YingtongAamandaWu , I don't believe the sequence headers are the issues, but instead the RDP classification output may not be consistent with the expected format. Can you upload |
Thanks for the timely response. From my side, the otu_taxonomy.rdp is an empty file: |
It appears that one of the files produced by RDP when training was not present at the time of classification. You will need to retrain the classifier, using |
Yes, that was exactly why. I used 8GB at first, and then I used 128GB and it ran. Thank you for helping! |
Dear all,
I have been trying to test Constax, but I have been facing a problem, which I think might be related to the pathfile, but I have not been able to figure out a solution. I installed constax in a conda environment using the commands given in the instructions and I have constax v2.0.9 installed in a Ubuntu server, v 18.04.5 LTS.
I have tried to run constax both with and without indicating the pathfile that is located in the conda environment (the result is the same). My code looks like:
and I get the following output
Perhaps there is some simple mistake that I am making?
thanks for any help
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