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.
While trying to run AA, I received the following error:
[root:INFO] #TIME 4205.320 Reconstructing amplicon1
[root:INFO] #TIME 4205.320 Calculating coverage meanshift segmentation
[root:INFO] #TIME 4205.320 Detecting breakpoint edges
[root:INFO] #TIME 4205.320 Building breakpoint graph
[root:INFO] #TIME 4209.130 Optimizing graph copy number flow
Traceback (most recent call last):
File "//data/wangyong/AmpliconArchitect/src/AmpliconArchitect.py", line 300, in
bamFileb2b.interval_filter_vertices(ilist, amplicon_name=amplicon_name, runmode=args.runmode)
File "/gpfs/gsfs7/users/wangyong/AmpliconArchitect/src/bam_to_breakpoint.py", line 2163, in interval_filter_vertices
task.putSCeval(opro, oprjo, oprfo, oprgo, oprho)
File "/data/wangyong/mosek/8/tools/platform/linux64x86/python/3/mosek/init.py", line 2181, in putSCeval
load_scopt()
File "/data/wangyong/mosek/8/tools/platform/linux64x86/python/3/mosek/init.py", line 951, in load_scoptscopt = __libraryfactory(os.path.join(dlldir,makelibname('mosekscopt%d%d' % (mskmajorver.value,mskminorver.value))))
File "/usr/local/bin/../Anaconda/envs/py2.7/lib/python2.7/posixpath.py", line 70, in join
elif path == '' or path.endswith('/'):
AttributeError: 'NoneType' object has no attribute 'endswith'
I used python/2.7 and version of mosek is 8. Could you please let me know how to solve the problem. I also tried python/3.6, 3.7, 3.8, all gave different kinds of error.
Thanks
While trying to run AA, I received the following error:
[root:INFO] #TIME 4205.320 Reconstructing amplicon1 [root:INFO] #TIME 4205.320 Calculating coverage meanshift segmentation [root:INFO] #TIME 4205.320 Detecting breakpoint edges [root:INFO] #TIME 4205.320 Building breakpoint graph [root:INFO] #TIME 4209.130 Optimizing graph copy number flow Traceback (most recent call last):
bamFileb2b.interval_filter_vertices(ilist, amplicon_name=amplicon_name, runmode=args.runmode)
File "/gpfs/gsfs7/users/wangyong/AmpliconArchitect/src/bam_to_breakpoint.py", line 2163, in interval_filter_vertices
task.putSCeval(opro, oprjo, oprfo, oprgo, oprho)
File "/data/wangyong/mosek/8/tools/platform/linux64x86/python/3/mosek/init.py", line 2181, in putSCeval
load_scopt()
File "/data/wangyong/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 "/usr/local/bin/../Anaconda/envs/py2.7/lib/python2.7/posixpath.py", line 70, in join
elif path == '' or path.endswith('/'):
AttributeError: 'NoneType' object has no attribute 'endswith'
File "//data/wangyong/AmpliconArchitect/src/AmpliconArchitect.py", line 300, in
I used python/2.7 and version of mosek is 8. Could you please let me know how to solve the problem. I also tried python/3.6, 3.7, 3.8, all gave different kinds of error. Thanks