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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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AttributeError: Task instance has no attribute 'putSCeval' #124

Closed ZHONGHONGXIN closed 1 year ago

ZHONGHONGXIN commented 1 year ago

hi,l am running AA, and my commend is:

Commandline: ./software/AmpliconArchitect/src/AmpliconAbed ./cnvkit/skmes1_noref/cnv_5_d.bed
--bam ./skmes1_pe_redup.bam --sensitivems False --ref GRCh38 --out cnv_5

when optimizing graph copy number flow , the errow follow in blow: Traceback (most recent call last): File "./software/AmpliconArchitect/src/AmpliconArchitect.py", line 28 bamFileb2b.interval_filter_vertices(ilist, amplicon_name=amplicon_name, runmode=args.runmode File "./software/AmpliconArchitect/src/bam_to_breakpoint.py", line 21_filter_vertices task.putSCeval(opro, oprjo, oprfo, oprgo, oprho) AttributeError: Task instance has no attribute 'putSCeval'

Could you please provide me any suggestions?

Thanks, ZHX

jluebeck commented 1 year ago

Hi, this error will arise when the wrong version of Mosek is used. AA supports Mosek 8, which has installation instructions available in step 4 here.

Cheers, Jens

ZHONGHONGXIN commented 1 year ago

Hi, this error will arise when the wrong version of Mosek is used. AA supports Mosek 8, which has installation instructions available in step 4 here.

Cheers, Jens

Thanks for you reply!