Error with matching_distance function in iPython example

[miladkiaee]

Do you know what might have caused the following error when I try to replicate what is shown in your ipython example with the matching_distance function? I managed to get the same results on all other parts of the notebook. I am using Linux and a Python 3.7 under Conda environment. Thanks!

Error in file /tmp/tmpahk85_rb/self.txt, line number 15: cannot parse "--"
ERROR:root:Failure in invocation of Hera, input files copied to error-hera-yellow-31885-1553538069.0262306 for reference
Traceback (most recent call last):
  File "/home/milad/anaconda3/envs/myenvpy37/lib/python3.7/site-packages/pyrivet/hera.py", line 86, in multi_bottleneck_distance
    ["bottleneck_dist", t1_name, t2_name, str(relative_error)])
  File "/home/milad/anaconda3/envs/myenvpy37/lib/python3.7/subprocess.py", line 395, in check_output
    **kwargs).stdout
  File "/home/milad/anaconda3/envs/myenvpy37/lib/python3.7/subprocess.py", line 487, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['bottleneck_dist', '/tmp/tmpahk85_rb/self.txt', '/tmp/tmpahk85_rb/other.txt', '1e-10']' returned non-zero exit status 1.
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/milad/anaconda3/envs/myenvpy37/lib/python3.7/site-packages/pyrivet/matching_distance.py", line 99, in matching_distance
    [bars for (_, bars) in multi_bars2]
  File "/home/milad/anaconda3/envs/myenvpy37/lib/python3.7/site-packages/pyrivet/hera.py", line 86, in multi_bottleneck_distance
    ["bottleneck_dist", t1_name, t2_name, str(relative_error)])
  File "/home/milad/anaconda3/envs/myenvpy37/lib/python3.7/subprocess.py", line 395, in check_output
    **kwargs).stdout
  File "/home/milad/anaconda3/envs/myenvpy37/lib/python3.7/subprocess.py", line 487, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['bottleneck_dist', '/tmp/tmpahk85_rb/self.txt', '/tmp/tmpahk85_rb/other.txt', '1e-10']' returned non-zero exit status 1.

[xoltar]

Based on this part of the error message:

Error in file /tmp/tmpahk85_rb/self.txt, line number 15: cannot parse "--"

My first guess would be that you installed Hera either not from the xoltar fork, or else you did use the xoltar fork, but didn't check out the c-api branch before building.

The original Hera code only supports processing a single pair of barcodes, but for efficiency we want to compare many pairs in a single invocation. These multiple pairs are separated by the "--" separator. The c-api branch in the xoltar fork of Hera contains the code that knows how to process these.

Please let me know if this does or doesn't solve the problem.

[miladkiaee]

I actually used your forked version of hera with the c_api.
My guess would be that I am doing something wrong with the cmake when I am building the bottleneck_dist. What I am doing is simply uncommenting the two commented lines in the CMakeList.txt and building the app bottlleneck_dist and the library libbottleneck.a. I thought there might be something there I am missing. I also tried to reinstall the python-rivet in case something went wrong there but that didn't help as of yet.