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elzbth / jitterbug

Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.
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installation error #24

Open AnneJRomero opened 1 year ago

AnneJRomero commented 1 year ago

I have installed jitterbug and I have the conda environment with the required dependencies:

psutil 5.7.0 py27hdf8410d_1 conda-forge pybedtools 0.8.1 py27h4bd9754_2 bioconda pysam 0.16.0.1 py27ha863e18_1 bioconda python 2.7.15 h5a48372_1011_cpython conda-forge

but when testing it out I get the following error: (TE27) [ar14g12@cyan51 jitterbug]$ jitterbug.py ../bam_files/D_L2_sort.bam ../TE_annotation/TE_anno.gff3 Traceback (most recent call last): File "./jitterbug.py", line 21, in from Run_TE_ID_reseq import File "/mainfs/scratch/ar14g12/PhD/tomato/TE/jitterbug/jitterbug/Run_TE_ID_reseq.py", line 6, in import pysam File "/home/ar14g12/.local/lib/python2.7/site-packages/pysam/init.py", line 5, in from pysam.libchtslib import ImportError: /home/ar14g12/.local/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: PyUnicodeUCS2_DecodeUTF8

Googling the error it looks like there is a mismatch between the python installation and the package, one being encoded in unicodeUSC2 and the other in USC4.
https://stackoverflow.com/questions/11878666/python-undefined-symbol-pyunicodeucs2-decodeutf8

Do you have a quick fix for this problem?

hanshanmengqi commented 4 months ago

Hi @AnneJRomero,

I think it's probably because of the version of dependencies. In my case, I downloaded the dependencies as shown below:

matplotlib 2.2.5
matplotlib-base 2.2.5
matplotlib-venn 0.11.5
memory-profiler 0.41
numpy 1.15.4 pandas 0.24.2 pybedtools 0.7.10 pysam 0.8.4 python 2.7.15 setuptools 44.0.0

Hope it's helpful.

Han