make test problem with python

[zmz1988]

Hi there!

I recently installed katulai and tried running 'make test'. After 'make test', I got this error:

(omit info of installation of many packages...) Using /share/apps/miniconda3/lib/python3.8/site-packages/wcwidth-0.2.5-py3.8.egg Searching for smmap==3.0.5 Best match: smmap 3.0.5 Processing smmap-3.0.5-py3.8.egg smmap 3.0.5 is already the active version in easy-install.pth

Using /share/apps/miniconda3/lib/python3.8/site-packages/smmap-3.0.5-py3.8.egg Finished processing dependencies for katuali==0.3.2 mkdir -p test/MinIonRun1 . ./venv/bin/activate && cd test/MinIonRun1 && katuali_datafile test/reads.tgz | xargs -I {} tar -xf {} /bin/sh: /share/apps/katuali/venv/bin/katuali_datafile: /share/apps/katuali/venv/bin/python: bad interpreter: No such file or directory mkdir -p test/MinIonRun2 . ./venv/bin/activate && cd test/MinIonRun2 && katuali_datafile test/reads.tgz | xargs -I {} tar -xf {} /bin/sh: /share/apps/katuali/venv/bin/katuali_datafile: /share/apps/katuali/venv/bin/python: bad interpreter: No such file or directory mkdir -p test/GridIonRun1 . ./venv/bin/activate && cd test/GridIonRun1 && katuali_datafile test/reads.tgz | xargs -I {} tar -xf {} /bin/sh: /share/apps/katuali/venv/bin/katuali_datafile: /share/apps/katuali/venv/bin/python: bad interpreter: No such file or directory mkdir -p test/GridIonRun2 . ./venv/bin/activate && cd test/GridIonRun2 && katuali_datafile test/reads.tgz | xargs -I {} tar -xf {} /bin/sh: /share/apps/katuali/venv/bin/katuali_datafile: /share/apps/katuali/venv/bin/python: bad interpreter: No such file or directory . ./venv/bin/activate && cd test && katuali -s Snakefile --configfile config.yaml --printshellcmds -j 48 --config THREADS_PER_JOB=48 MinIonRun1/guppy/basecalls.fastq.gz /share/apps/katuali/venv/bin/katuali: /share/apps/katuali/venv/bin/katuali_datafile: /share/apps/katuali/venv/bin/python: bad interpreter: No such file or directory /share/apps/katuali/venv/bin/katuali: /share/apps/katuali/venv/bin/katuali_datafile: /share/apps/katuali/venv/bin/python: bad interpreter: No such file or directory /share/apps/katuali/venv/bin/katuali: /share/apps/katuali/venv/bin/katuali_datafile: /share/apps/katuali/venv/bin/python: bad interpreter: No such file or directory

/share/apps/katuali/venv/bin/katuali: /share/apps/katuali/venv/bin/process_katuali_config: /share/apps/katuali/venv/bin/python: bad interpreter: No such file or directory Running snakemake -s Snakefile --configfile configs/katuali_2021-03-15_15:33:05+00:00.yaml --restart-times 0 --keep-going --printshellcmds -j 48 MinIonRun1/guppy/basecalls.fastq.gz
Config saved to configs/katuali_2021-03-15_15:33:05+00:00.yaml bash: /share/apps/katuali/venv/bin/snakemake: /share/apps/katuali/venv/bin/python: bad interpreter: No such file or directory make: *** [test_basecall] Error 126

It seems that python causes the problem. But I have my python in /share/apps/miniconda3/bin/python, and the version is 3.8.5. I tried to copy the executable to /share/apps/katuali/venv/bin/, as suggested in other posts, but it got me an error: "cp: not writing through dangling symlink ‘/share/apps/katuali/venv/bin/python’ "

Could you please tell me how I can copy the python executable to the right folder, if this is the cause of the problem? If not, could you please help me solve this problem?

Thanks a lot for your time!

[cjw85]

It looks like the test rull in the make file isn't quite correct. Your issue will be alleviated by running:

make venv/bin/activate test

[zmz1988]

Thanks for the fast reply! I tried the line you suggested, but got the same error as before...