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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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Always stuck at "Optimizing graph copy number flow" #127

Open szbssg opened 1 year ago

szbssg commented 1 year ago

Hi,I tried run AA with the outputs of AApipeline many times.And I always stuck at "Optimizing graph copy number flow". And this is the error. image [root:INFO] [amplicon6] chr11:72963773-74145256 [root:INFO] [amplicon7] chr11:74950122-75435051,chr11:76219931-76724864,chr11:99412587-102307510 [root:INFO] #TIME 15520.911 Reconstructing amplicon1 [root:INFO] #TIME 15520.932 Calculating coverage meanshift segmentation [root:INFO] #TIME 15534.923 Detecting breakpoint edges (interval filter vertices) [root:INFO] #TIME 15585.946 Building breakpoint graph [root:INFO] #TIME 15587.706 Optimizing graph copy number flow Traceback (most recent call last): File "/home/u22211230020/PAA/AmpliconArchitect/src/AmpliconArchitect.py", line 321, in bamFileb2b.interval_filter_vertices(ilist, amplicon_name=amplicon_name, runmode=args.runmode) File "/home/u22211230020/PAA/AmpliconArchitect/src/bam_to_breakpoint.py", line 2192, in interval_filter_vertices task.putSCeval(opro, oprjo, oprfo, oprgo, oprho) File "/home/u22211230020/mosek/8/tools/platform/linux64x86/python/3/mosek/init.py", line 2181, in putSCeval load_scopt() File "/home/u22211230020/mosek/8/tools/platform/linux64x86/python/3/mosek/init.py", line 951, in load_scopt scopt = __libraryfactory(os.path.join(dlldir,makelibname('mosekscopt%d%d' % (mskmajorver.value,mskminorver.value)))) File "/home/u22211230020/.conda/envs/py39/lib/python3.9/posixpath.py", line 76, in join a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType

And , it really disturbed me a lot.My python is Python version 3.9.13 (main, Oct 13 2022, 21:15:33), My AA is AmpliconArchitect version 1.3.r2.Is there any problem about python?.Looking forward to your reply.

jluebeck commented 1 year ago

Hi,

Thanks for sharing this error. It is possible this is related to your mosek installation. A few questions:

  1. What was the exact AA command you ran?
  2. It's possible mosek 8 is not compatible with python3.9. You may want to try installing python2 or a lower version of python 3. We have a development version of AA that may avoid this error here: https://github.com/jluebeck/AmpliconArchitect/tree/unstable_dev
  3. Can you confirm your mosek version by opening a python interactive session and do the following import mosek mosek.Env.getversion() and reporting the output?
  4. You can also try uninstalling and reinstalling mosek to see if this error persists.
  5. You could also see if you are getting the same behavior from this small test sample https://www.ncbi.nlm.nih.gov/sra/?term=FF-17

Thanks Jens

Roman-Sig commented 1 year ago

I also encountered the same problem, but things went smoothly after I switched to python 2.7 (I was using python 3.8.8) and built dependencies like instructed in the AA manual. Yay! Thanks, Jens :) Jingwen