Error with k-mer repeat count calculations; terminating program. about mantis HOT 9 CLOSED

Although I have not yet been able to reproduce this issue, I suspect that this is the sequence of events:

1. Calling python from the shell to run mantis.py triggers the bash alias to python3. As Python 3.5 runs with PYTHONPATH pointing to the 3.5 libraries, it runs fine.
2. mantis.py calls a helper program kmer_repeat_counter.py. However, bash will only recognize alias if run through an interactive shell (as explained here). Therefore, Python 2.7 runs kmer_repeat_counter.py.
3. PYTHONPATH is still pointing to the 3.5 libraries. Given syntactic differences between Python 2 and 3, Python 2.7 crashes upon attempting to import them.

This issue should be fixed by properly packaging MANTIS (see #20). Until then, this may be a potential workaround:

1. Create a folder in your home directory.
2. Softlink /usr/local/bin/python3.5 to a link named 'python' in that folder.
3. Set PATH to contain that folder first (e.g. export PATH=/path/to/python_folder:$PATH)
4. Keep using your PYTHONPATH variable.

from mantis.

What command are you using to run MANTIS? Also, please run 'python -V' and post the output.

from mantis.

Thanks for your help.

Here is the command:
python mantis.py --bedfile msi.test.bed --genome /Volumes/Data/References/HiSeqAnalysisSoftware_UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -n ./Sample-N1-EX-KD.bam -t ./Sample-T1-EX-KD.bam -o msi.txt

pgmserver01 ~/MANTIS-master -> python -V
Python 3.5.1

from mantis.

We are investigating this; we are currently requesting to borrow a Mac (from our department) to attempt to reproduce your error.

from mantis.

The only other reference to this error I can find is https://stackoverflow.com/questions/38124761/import-site-failed-use-v-for-traceback

Which python are you using? Can you also show the output of which python and which python3?

from mantis.

from mantis.

Try this version: https://github.com/rbonneville/MANTIS/tree/iss021

from mantis.

Hello @jp3117, do you have any further questions regarding this issue?

from mantis.

from mantis.