The bioBakery help forum

Can not call software version for bowtie2

When I use humann2, it shows can not call software version for bowtie2, how can I solve this problem

Hello, Try running $ bowtie2 --version to see if there is an issue with your bowtie2 install. If there is an issue if you would resolve it by possibly installing bowtie2 again it should resolve the HUMAnN error.

Thank you,
Lauren

Hello,thanks for your helping.

Hello,if I install bowtie2 again,can I use humann2 -i -o to analyze the data or I should run bowtie2 first then analyze the result from bowtie2 by humann2.

Hello, If you install bowtie2 again I would first run $ bowtie2 --version to make sure that the install is okay. If it is okay, then run HUMAnN and the original error should have been resolved.

Thank you,
Lauren

Hello,thanks for your helping,but when I run humann2 -i -o,It shows
Running metaphlan2.py …

Traceback (most recent call last):
File “/home/xianzhang/miniconda2/envs/meta/bin/humann2”, line 11, in
sys.exit(main())
File “/home/xianzhang/miniconda2/envs/meta/lib/python2.7/site-packages/humann2/humann2.py”, line 900, in main
bug_file = prescreen.alignment(args.input)
File “/home/xianzhang/miniconda2/envs/meta/lib/python2.7/site-packages/humann2/search/prescreen.py”, line 72, in alignment
utilities.execute_command(exe, args, [input], [bug_file, bowtie2_out])
File “/home/xianzhang/miniconda2/envs/meta/lib/python2.7/site-packages/humann2/utilities.py”, line 740, in execute_command
message+="\nError message returned from " + os.path.basename(exe) + " :\n" + e.output.decode(“utf-8”)
UnicodeDecodeError: ‘ascii’ codec can’t decode byte 0xe5 in position 124: ordinal not in range(128)
I want to know what does the problem mean and how to solve it .

Hello, Thank you for the follow up. It looks like there are some unexpected characters in the error message that the code is having an issue decoding to print to standard output.

The command that ran into the error should be printed to your log file. If you would check your log file for the last line that includes Execute command: and the run that command directly on the command line it should give us the error message. Feel free to post it and I can help debug from there.

Thank you,
Lauren