CLEAR: python2 or python3?

[nliorni]

Greetings,

I tried to use the CLEAR pipeline under a python3 environment, and it worked well until the TopHat, where I got:

TopHat2 is not compable to python3. You can change to a python2 environment or change tophat shebang "#!/usr/bin/env python" to "#!/usr/bin/env python2"

Therefore, I created a python2 environment as suggested. This time I couldn't even got to the TopHat step, getting an error as soon as I launched CLEAR:

File "/opt/miniconda3/envs/TopHat/lib/python2.7/site-packages/pybedtools/contrib/long_range_interaction.py", line 357 print("%d (%.1f%%)\r" % (c, c / float(n) * 100), end="")
What can I do to solve the issue. Thanks in advance

nl

[wangmengbo]

Greetings,

I tried to use the CLEAR pipeline under a python3 environment, and it worked well until the TopHat, where I got:

TopHat2 is not compable to python3. You can change to a python2 environment or change tophat shebang "#!/usr/bin/env python" to "#!/usr/bin/env python2"

Therefore, I created a python2 environment as suggested. This time I couldn't even got to the TopHat step, getting an error as soon as I launched CLEAR:

File "/opt/miniconda3/envs/TopHat/lib/python2.7/site-packages/pybedtools/contrib/long_range_interaction.py", line 357 print("%d (%.1f%%)\r" % (c, c / float(n) * 100), end="") What can I do to solve the issue. Thanks in advance

nl

I met the same exact error although I was running circ_quant directly. It seems not working with at least pybedtools v0.9.0.

[nliorni]

I dropped :\

[Si-Nan]

dependencies:

• Python2
• Circexplorer2
• Hisat2
• stringTie
• Pysam
• pybedtools
• Bowtie # v1.1.2 is ok
• Samtools == 0.1.9 # https://sourceforge.net/projects/samtools/files/samtools/0.1.9/samtools-0.1.9.tar.bz2
• Tophat == 2.1.0 # http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.Linux_x86_64.tar.gz
• Ucsc-genepredtogtf
• Ucsc-gtftogenepred