# Run biobakery\_workflows wmgx example failed, maybe some problems in shotgun.py

**URL:** <https://forum.biobakery.org/t/run-biobakery-workflows-wmgx-example-failed-maybe-some-problems-in-shotgun-py/3666>\
**Category:** bioBakery workflows\
**Created:** [May 31, 2022, 12:57am UTC](https://forum.biobakery.org/t/run-biobakery-workflows-wmgx-example-failed-maybe-some-problems-in-shotgun-py/3666 "2022-05-31T00:57:41Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![PeiJenWang](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/peijenwang/32/1484_2.png) [@PeiJenWang](https://forum.biobakery.org/u/PeiJenWang)\
**Post date:** [May 31, 2022, 12:57am UTC](https://forum.biobakery.org/t/run-biobakery-workflows-wmgx-example-failed-maybe-some-problems-in-shotgun-py/3666/1 "2022-05-31T00:57:41Z")

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First, this is the error message:

2022-05-30 17:40:46,756 LoggerReporter task\_failed ERROR: task 35, strainphlan\_print\_clades : Failed! Error message : Error executing action 0. Original Exception:  
Traceback (most recent call last):  
File “/usr/local/lib/python3.6/dist-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally  
action\_func(task)  
File “/usr/local/lib/python3.6/dist-packages/anadama2/helpers.py”, line 89, in actually\_sh  
ret = \_sh(s, \*\*kwargs)  
File “/usr/local/lib/python3.6/dist-packages/anadama2/util/ **init**.py”, line 320, in sh  
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))  
anadama2.util.ShellException: [Errno 1] Command `strainphlan --samples XXX/biobakery\_workflows/workflow\_output/strainphlan/_/_.pkl --output\_dir XXX/biobakery\_workflows/workflow\_output/strainphlan --print\_clades\_only \> XXX/biobakery\_workflows/workflow\_output/strainphlan/clades\_list.txt ’ failed.  
Out: b’’  
Err: b’\n[e] The main inputs samples + references are less than 4\nMon May 30 17:40:46 2022: Stop StrainPhlAn 3.0 execution.\n’

And I tried to change all the codes in shotgun.py …  
from

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/f/f8e37ea3199ff5cf77ed19b01c78f986ffbee2a2.png)  
to  
 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/6/60d43301e4363acbee0cbf3c4fc1c424d819dc21.png)  
because I thought it should be the same as  
 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/a/aa3076cdccf1ea1fc78f2c7dfa2986353da04fc1.png)

but still got the same error ~

And I’m guessing that maybe the problem is right here…

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/4/4307dc5c7a5c28e309c376b9915af0a5e2691cee.png)

Are you free to help me out? Thanks a lot !