Error: Bowtie2 or BEDTools not loaded

[ConYel]

Dear RepEnrich team,
I would like to use RepEnrich2 tool.
I have installed everything and I included everything in my $PATH.
I still get this error:

File "RepEnrich2_setup.py", line 40
    print "Error: Bowtie2 or BEDTools not loaded"
                                                ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Error: Bowtie2 or BEDTools not loaded")?

My version of Bowtie2 is :

/home/rstudio/Documents/gitstaff/bowtie2-2.3.5.1-linux-x86_64/bowtie2-align-s version 2.3.5.1 64-bit Built on Wed Apr 17 02:50:12 UTC 2019 Compiler: gcc version 7.3.1 20180303 (Red Hat 7.3.1-5) (GCC) Options: -O3 -m64 -msse2 -funroll-loops -g3 -g -O2 -fvisibility=hidden -I/hbb_exe_gc_hardened/include -ffunction-sections -fdata-sections -fstack-protector -D_FORTIFY_SOURCE=2 -fPIE -std=c++98 -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
I tried to find Bowtie2 version 2.2.9 in bioconda but there is only :

2.3.5-0, 2.3.4.3-1, 2.3.4.3-0, 2.3.4.2-0, 2.3.4.1-1, 2.3.4.1-0, 2.3.4-0, 2.3.3.1-0, 2.3.2-1, 2.3.0-1,

2.3.0-0, 2.2.8-2, 2.2.8-1

Is there something I could do?

Thank you in advance,
Con

[nskvir]

Hi there,

Which version of Python are you using?

[ConYel]

Python 3.7.2

[nskvir]

Ah, that's almost certainly the issue - RepEnrich2 was written with Python 2 (as opposed to Python 3). There are a lot of major syntax differences between the two, so if you try running with a version of Python starting with 2.7.x it should run properly. Apologies if this was ambiguous from the readme!

Best,
Nick

[ConYel]

Thank you, I'll test it and let you know!

[ConYel]

Traceback (most recent call last):
  File "/home/rstudio/Documents/gitstaff/RepEnrich2/RepEnrich2_setup.py", line 8, in <module>
    from Bio import SeqIO
ImportError: No module named Bio
python --version
Python 2.7.15

Now this

Don't mind this ^ it was not installed in the 2.7 python version the Biopython.

• Another question, I would like to know about the indexes of Bowtie2, do I have to recreate the indexes with lower offrate if I want?

[nskvir]

Yes, it seems like you'd probably have to rerun the setup step and modify the --offrate value in the script to build new indices if that's what you need. I personally have never done this though, so I can't really say what kind of effects it would have on things like run-time.

Hope this helps!
-Nick

[ConYel]

Thanks!
Last question I hope,
I run the
RepEnrich2_setup.py
setup and it's running for 478 min
99.7 9.1 478:48.25 python
I get :

Returning from initFromVector

Wrote 4488169 bytes to primary EBWT file: /home/rstudio/Documents/Databases/setup_folder_hg38/MamGypLTR3a.rev.1.bt2
Wrote 200944 bytes to secondary EBWT file: /home/rstudio/Documents/Databases/setup_folder_hg38/MamGypLTR3a.rev.2.bt2
Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor
Headers: len: 803744 bwtLen: 803745 sz: 200936 bwtSz: 200937 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 50235 offsSz: 200940 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 4187 numLines: 4187 ebwtTotLen: 267968 ebwtTotSz: 267968 color: 0 reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00
processing repgenome AluJr.fa (8350 of 14942)

Is there a problem with the setup?

[nskvir]

Looks like it's running normally to me - as long as it's not throwing any errors and is generating non-empty files in the setup folder I'd just wait for it to finish.

[ConYel]

Thanks for everything!!!