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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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ipdSummary: Chemistry cannot be identified---cannot perform kinetic analysis #80

Open wxie-18 opened 4 years ago

wxie-18 commented 4 years ago

when I run : ipdSummary aligned_subreads.bam --reference ~/genome/fruit_fly/fly.fasta --gff basemods.gff --csv basemods.csv

get the following error:

[ERROR] Chemistry cannot be identified---cannot perform kinetic analysis Chemistry cannot be identified---cannot perform kinetic analysis Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/pbcommand-1.8.6-py2.7.egg/pbcommand/cli/core.py", line 151, in _pacbio_main_runner return_code = exe_main_func(*args, *kwargs) File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 699, in args_runner return kt.start() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 412, in start return self.run() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 475, in run ret = self._mainLoop() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 629, in _mainLoop self.args.paramsPath) File "/usr/lib/python2.7/dist-packages/kineticsTools/internal/basic.py", line 26, in getIpdModelFilename raise Exception(msg) Exception: Chemistry cannot be identified---cannot perform kinetic analysis 2020-10-27 15:20:33,041 [ERROR] Chemistry cannot be identified---cannot perform kinetic analysis Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/pbcommand-1.8.6-py2.7.egg/pbcommand/cli/core.py", line 151, in _pacbio_main_runner return_code = exe_main_func(args, **kwargs) File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 699, in args_runner return kt.start() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 412, in start return self.run() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 475, in run ret = self._mainLoop() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 629, in _mainLoop self.args.paramsPath) File "/usr/lib/python2.7/dist-packages/kineticsTools/internal/basic.py", line 26, in getIpdModelFilename raise Exception(msg) Exception: Chemistry cannot be identified---cannot perform kinetic analysis

GDelevoye commented 3 years ago

Hi,

I'm not from PacBio and this question is from ~6 months ago, but in case it is still not solved for you, maybe you can download directly the ipdSummary from smrt-analysis instead

Everything has switched to python3 in the latest versions in this repo, and old models used in python2 are not supported anymore apparently

GDelevoye commented 2 years ago

Once more 6 month later : I had a similar issue and I fixed it by using intercompatible versions of BLASR and kineticsTools (that was the problem for me) from a same version of Smrtanalysis, and also by specifying the path to the in-silico model manually (SP2-C2, P6-C4, etc, which are all present in the repo)

Note that these in-silico models 1) depend on your chemistry and 2) the way the PacBio tools handles them (location, file format, necessity to indicate them, etc) has changed from one version to another hence the importance of using compatible softwares. There is also a version of the sequencer for which no valid in-silico control has been developed (Sequel II.v1)

If you want to use your own fork of ipdSummary, on my Sequel I data I managed to make everything compatible using the following dependencies: