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pysam.cfaidx.FastqProxy has the wrong size, try recompiling #45
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Hi Nikolas, I haven't seen specifically this error before, but I think things like this can happen if there are multiple version of pysam installed on a computer, and there is any inconsistency between the version of pysam that pysamstats was built against and the version of pysam that is installed when you run a particular python interpreter. The only thing I can suggest is to try installing into a virtual environment. Start with a clean virtual environment, upgrade pip and setuptools to ensure you have the latest, then install cython, numpy, pysam and pysamstats, all via pip. If that still doesn't work, let me know. Hth. |
Same error confirmed, python 2.7, new virtual env, and pip install or install from source |
Thanks, looking into it. |
If I remember correctly I think this happened because I was in the |
Thanks @pontikos but may be a different problem (with same error message), looks like pysam 0.8.4 moved a couple of things, am just testing a new pysamstats release which should fix. |
Hi @luwening, I've released a new version 0.24.0 which should be compatible with pysam 0.8.4. Could you make sure you have pysam 0.8.4 installed, then try installing pysamstats? Thanks. |
I'm having the same issues with the latest version of both pysam (0.9.0) and pysamstats (0.24.2). It's not really possible for me to reinstall everything but I have the latest version of cython and numpy as well. Any idea why it would be doing this? |
Hi there, I have not checked compatibility with pysam 0.9.0 yet, apologies. On Wednesday, 23 March 2016, Kenneth Smith <notifications@github.com
Alistair Miles |
@alimanfoo Any idea of when pysamstats will support more recent pysam versions? |
Apologies, I'm absolutely snowed under at the moment. It's good to know you On Wednesday, May 11, 2016, astewart-twist notifications@github.com wrote:
Alistair Miles |
I was just asking out of curiosity @alimanfoo. I'm more curious to see how any pileup computation changes between samtools 2 and 3 would affect pysamtools calculations. I'd be happy to test out compatibility in the meantime. Is it fairly straight forward to force pysamtools to use pysam > 0.8.4 (or samtools > 2 directly) ? |
You could try compiling pysamstats current master against pysam latest release, you would just need to set up a virtual environment where the new pysam is installed, then clone pysamstats repo and build:
I don't know if or how the pysam cython API has changed since 0.8.4 so you will probably get compile errors. If it's not obvious how to resolve them then feel free to drop the error logs here, I'd be happy to help diagnose. |
Hello I've cloned the git repo on my local machine and I'm this is the warning when I attempt to install pysamstats:
Later when I try to import the package I get this error:
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