When I try to run a local version of DeepPotential I continuously get the following error:
python DeepPotential.py final.a3m final
cuda is ready? : False
Traceback (most recent call last):
File "/Applications/DeepPotential/DeepPotential.py", line 189, in <module>
prepare_longdistance(alnfile,savefile)
File "/Applications/DeepPotential/DeepPotential.py", line 112, in prepare_longdistance
fea_1d_,fea_2d_=features.collect_allfeatures(msafile,savefile_)
File "/Applications/DeepPotential/features.py", line 331, in collect_allfeatures
plm=getpotts(testaln,outprefix,istraining)
File "/Applications/DeepPotential/features.py", line 105, in getpotts
plm=read_potts(stdout,length)
File "/Applications/DeepPotential/features.py", line 71, in read_potts
vec=np.genfromtxt(BytesIO(lines[l1+(states+1)*(count-1)+1+j]))
IndexError: list index out of range
I have tried this with multiple MSA files in A3M format, to ensure that it's not an issue with the specific MSA. Any help in resolving the issue would be appreciated.
A sample MSA I've tried and received the same error is below:
>MspA
AEPAAEAKVAEFSGNAAVTFGFDLDTVKAGFKNTTEADLKFNLMNGGDKSTTGNGVWGELKLVVNALQIRATADVSDGHTFAIQTKKDNDGEDTIFVEIDTAKLHFNDLYVGITSGDFRYGGSFWYPNALNYKDSKEDEKYTRSRAAKLGYDQGLVLGYEKKDLFKVELAARSKKDTTKKVEKVELVHLSAGAKIKEKEYYKTEPAAVTGDTAQDIFNDGTLVSVTADPKVKTLNAEGAYYKPVMKDDETNYWTNKFALGLYGEVTPIKDLRIGVGAAYVLGQLGAAASEDDKTNDISVFAGVDYRFNFNEDFFIQPTVTYNFYNDYKVASKNYAIETNKMNAGLRFGFAKSKSDSENESLLYTFFGQEKLFYETTKNDKGDQILLPGVSVFGSFNFKENAMKTELPVMLTFYSGELVQNLKAYALFGANLGPDAGKGTAVAMSDAVYKGIIEKKGMQAGLAASYDVKVNDAVTIVPAAGVLWTHGSQASGNDKMSADEVAVSLKADVKGLVSNTTFTAFWEKASFGKGAASVGGTKTSVDAVKKGVIGLKAKIAL
>tr|U2KQ42|U2KQ42_TRELE Major outer membrane protein MspA OS=Treponema lecithinolyticum ATCC 700332 GN=HMPREF9193_00379 PE=4 SV=1
DEPSAEAKIAEFKGDAAVTFGVDLDTNRTGFKNEVGGSIKLNLLNGGDKSTTGDGIWGELKLKINAFTLQAKADKNVNLL----T---KIDDDDVKVEIDTAKIHIGPAYVGIKKGDLNYGSNFWYPNALNYKDGD-DEYYNRTPSDKVKYDQGLVLGYEQKDLFKVETAFRSQKDTGKKLDKVEGVILPKDTEIKKGEYFKSVEGAHDNAKTDDVFDDAALVDPiPGKTDVKKLKATKAVFKRVMKDGDTNYWTDKYALGVYGEVKPIKDLRVAIGTAYVFGRLSGDkdvlkaVGDSDNRGDITFFTGADYKLSLLEKFVVNPVVTYTLYADAKWNGADEklyypeDLKTSMLKTGVRFGWGEEK---KSNSLLYDFFGKNTLVYDTNKEDKGDDKLLPGVSLFGAFDLVNKNIETKLPLMMTFYSGELVKGLNVAALVHANVAKDASEIsrvvpgtvYAGRMTKADYERLIGAKGLQIGLAASYDVKLND-ITIVPAAAMLWTHGMLKGeADTRMTADEFKVEAKVDVKGVIQNTTLSVFWDEAAFGKGTSKEWtfgvkHDEQNYYTLKNGVFGLKAKIAL
>tr|F4LK31|F4LK31_TREBD Uncharacterized protein OS=Treponema brennaborense (strain DSM 12168 / CIP 105900 / DD5/3) GN=Trebr_2078 PE=4 SV=1
AEPVADVKIAEFSGNASVQWGVNLDSGKTGFLNAYEVVFKLNLLNNGTKSTTGDGVWGELVLKTDDDTFIGWKNTENSDGkFNANKGMQDGKNLGLKVFVDVAKIHLGPAYIGIKRGDTQTGELKMDA-AIRSSDDDQ--AKWLSNVGPDKFSQGIVVGFAN-DMFGIDVDLRSYAVDK-----------------------------------------------------------------TDSTDIVNQYTGAYAFAGEAEFKGVENLSIKAGASYNFSDKFYAntasdtS--ASLDTVLGYSASAGYKLALNDTYYIRPQVGFAGANSKTDA----nnSKSGMAMAFGVLFGWGEIGMDKNADVAF--------------LDDDMAKKVSPGVGVVAYVPFKGTSKVagvssdaeqlYTARIMPSFFSGEIVKNLTAAAYGDIVVMNDKYPTv----A--------NKDMGMAFVLSAKYAIPV-DAMTITPNAGVRFANASYADnykdfgeaddgvfgkkdgtyklsmgdqktktGSALFDGNFMNIKAGVDVAGLISNTTLSVIYESANVLNSLEAA----SGANVSKLGTLNFKAKIAL
>tr|F4LK33|F4LK33_TREBD Autotransporter beta-domain protein OS=Treponema brennaborense (strain DSM 12168 / CIP 105900 / DD5/3) GN=Trebr_2080 PE=4 SV=1
AEPVADVKIAEFSGNASVQWGVNLDSGKTGFLNAYEVVFKLNLLNNGTKSTTGDGVWGELVLKTDGDTFIGWKNTSYGDTaTKSGEGMT--SDLKLKTFVDVAKIHLGPAYIGIKSGDTRTGSLKMDA-AIRSADNDNafipvvsnednKTYNYLHDVGPKGFSQGIVAGFAN-DMFGIDVDLRSYEA-------------------------------------------------------------------------TTQYSNAYAFAAEAEFKGVENLSVKAGASYNFSDKYYNddtssvK--TSLANVMGYSASAGYKLALNDTYYIRPQVGFTGTNSTQTVAS--vetKSNSMDMAFGVLFGWGEIGMDKNADVPF--------------LDNDGAKKVSPGVSIHAAMPLAAKTGDtdylkdgRAIVLRPAFFSGEIVKNLTVAALADIVLPV-GYDN-------------NPDPMFGMVFGVKYAIAV-DAITVTPNFGVRFANKEYAAyakavvaenneslitrdwydgtteknaAINGSVDGIMNIKAGVDVAGLISNTTLSLIYESANLQNSKDYT----GTANPVKLGTLNLKAKIAL
DeepPotential "Index out of range"
Moderator: robpearc
Re: DeepPotential "Index out of range"
Dear user,
Can you post your a3m file as an attachment?
Best
IT Team
Can you post your a3m file as an attachment?
Best
IT Team
Re: DeepPotential "Index out of range"
When I try to attach the file, I get an error saying that the file type is invalid. I have attached the text below:
>seq
AEPAAEAKVAEFSGNAAVTFGFDLDTVKAGFKNTTEADLKFNLMNGGDKSTTGNGVWGELKLVVNALQIRATADVSDGHTFAIQTKKDNDGEDTIFVEIDTAKLHFNDLYVGITSGDFRYGGSFWYPNALNYKDSKEDEKYTRSRAAKLGYDQGLVLGYEKKDLFKVELAARSKKDTTKKVEKVELVHLSAGAKIKEKEYYKTEPAAVTGDTAQDIFNDGTLVSVTADPKVKTLNAEGAYYKPVMKDDETNYWTNKFALGLYGEVTPIKDLRIGVGAAYVLGQLGAAASEDDKTNDISVFAGVDYRFNFNEDFFIQPTVTYNFYNDYKVASKNYAIETNKMNAGLRFGFAKSKSDSENESLLYTFFGQEKLFYETTKNDKGDQILLPGVSVFGSFNFKENAMKTELPVMLTFYSGELVQNLKAYALFGANLGPDAGKGTAVAMSDAVYKGIIEKKGMQAGLAASYDVKVNDAVTIVPAAGVLWTHGSQASGNDKMSADEVAVSLKADVKGLVSNTTFTAFWEKASFGKGAASVGGTKTSVDAVKKGVIGLKAKIAL
>tr|U2KQ42|U2KQ42_TRELE Major outer membrane protein MspA OS=Treponema lecithinolyticum ATCC 700332 GN=HMPREF9193_00379 PE=4 SV=1
DEPSAEAKIAEFKGDAAVTFGVDLDTNRTGFKNEVGGSIKLNLLNGGDKSTTGDGIWGELKLKINAFTLQAKADKNVNLL----T---KIDDDDVKVEIDTAKIHIGPAYVGIKKGDLNYGSNFWYPNALNYKDGD-DEYYNRTPSDKVKYDQGLVLGYEQKDLFKVETAFRSQKDTGKKLDKVEGVILPKDTEIKKGEYFKSVEGAHDNAKTDDVFDDAALVDPiPGKTDVKKLKATKAVFKRVMKDGDTNYWTDKYALGVYGEVKPIKDLRVAIGTAYVFGRLSGDkdvlkaVGDSDNRGDITFFTGADYKLSLLEKFVVNPVVTYTLYADAKWNGADEklyypeDLKTSMLKTGVRFGWGEEK---KSNSLLYDFFGKNTLVYDTNKEDKGDDKLLPGVSLFGAFDLVNKNIETKLPLMMTFYSGELVKGLNVAALVHANVAKDASEIsrvvpgtvYAGRMTKADYERLIGAKGLQIGLAASYDVKLND-ITIVPAAAMLWTHGMLKGeADTRMTADEFKVEAKVDVKGVIQNTTLSVFWDEAAFGKGTSKEWtfgvkHDEQNYYTLKNGVFGLKAKIAL
>tr|F4LK31|F4LK31_TREBD Uncharacterized protein OS=Treponema brennaborense (strain DSM 12168 / CIP 105900 / DD5/3) GN=Trebr_2078 PE=4 SV=1
AEPVADVKIAEFSGNASVQWGVNLDSGKTGFLNAYEVVFKLNLLNNGTKSTTGDGVWGELVLKTDDDTFIGWKNTENSDGkFNANKGMQDGKNLGLKVFVDVAKIHLGPAYIGIKRGDTQTGELKMDA-AIRSSDDDQ--AKWLSNVGPDKFSQGIVVGFAN-DMFGIDVDLRSYAVDK-----------------------------------------------------------------TDSTDIVNQYTGAYAFAGEAEFKGVENLSIKAGASYNFSDKFYAntasdtS--ASLDTVLGYSASAGYKLALNDTYYIRPQVGFAGANSKTDA----nnSKSGMAMAFGVLFGWGEIGMDKNADVAF--------------LDDDMAKKVSPGVGVVAYVPFKGTSKVagvssdaeqlYTARIMPSFFSGEIVKNLTAAAYGDIVVMNDKYPTv----A--------NKDMGMAFVLSAKYAIPV-DAMTITPNAGVRFANASYADnykdfgeaddgvfgkkdgtyklsmgdqktktGSALFDGNFMNIKAGVDVAGLISNTTLSVIYESANVLNSLEAA----SGANVSKLGTLNFKAKIAL
>tr|F4LK33|F4LK33_TREBD Autotransporter beta-domain protein OS=Treponema brennaborense (strain DSM 12168 / CIP 105900 / DD5/3) GN=Trebr_2080 PE=4 SV=1
AEPVADVKIAEFSGNASVQWGVNLDSGKTGFLNAYEVVFKLNLLNNGTKSTTGDGVWGELVLKTDGDTFIGWKNTSYGDTaTKSGEGMT--SDLKLKTFVDVAKIHLGPAYIGIKSGDTRTGSLKMDA-AIRSADNDNafipvvsnednKTYNYLHDVGPKGFSQGIVAGFAN-DMFGIDVDLRSYEA-------------------------------------------------------------------------TTQYSNAYAFAAEAEFKGVENLSVKAGASYNFSDKYYNddtssvK--TSLANVMGYSASAGYKLALNDTYYIRPQVGFTGTNSTQTVAS--vetKSNSMDMAFGVLFGWGEIGMDKNADVPF--------------LDNDGAKKVSPGVSIHAAMPLAAKTGDtdylkdgRAIVLRPAFFSGEIVKNLTVAALADIVLPV-GYDN-------------NPDPMFGMVFGVKYAIAV-DAITVTPNFGVRFANKEYAAyakavvaenneslitrdwydgtteknaAINGSVDGIMNIKAGVDVAGLISNTTLSLIYESANLQNSKDYT----GTANPVKLGTLNLKAKIAL
>seq
AEPAAEAKVAEFSGNAAVTFGFDLDTVKAGFKNTTEADLKFNLMNGGDKSTTGNGVWGELKLVVNALQIRATADVSDGHTFAIQTKKDNDGEDTIFVEIDTAKLHFNDLYVGITSGDFRYGGSFWYPNALNYKDSKEDEKYTRSRAAKLGYDQGLVLGYEKKDLFKVELAARSKKDTTKKVEKVELVHLSAGAKIKEKEYYKTEPAAVTGDTAQDIFNDGTLVSVTADPKVKTLNAEGAYYKPVMKDDETNYWTNKFALGLYGEVTPIKDLRIGVGAAYVLGQLGAAASEDDKTNDISVFAGVDYRFNFNEDFFIQPTVTYNFYNDYKVASKNYAIETNKMNAGLRFGFAKSKSDSENESLLYTFFGQEKLFYETTKNDKGDQILLPGVSVFGSFNFKENAMKTELPVMLTFYSGELVQNLKAYALFGANLGPDAGKGTAVAMSDAVYKGIIEKKGMQAGLAASYDVKVNDAVTIVPAAGVLWTHGSQASGNDKMSADEVAVSLKADVKGLVSNTTFTAFWEKASFGKGAASVGGTKTSVDAVKKGVIGLKAKIAL
>tr|U2KQ42|U2KQ42_TRELE Major outer membrane protein MspA OS=Treponema lecithinolyticum ATCC 700332 GN=HMPREF9193_00379 PE=4 SV=1
DEPSAEAKIAEFKGDAAVTFGVDLDTNRTGFKNEVGGSIKLNLLNGGDKSTTGDGIWGELKLKINAFTLQAKADKNVNLL----T---KIDDDDVKVEIDTAKIHIGPAYVGIKKGDLNYGSNFWYPNALNYKDGD-DEYYNRTPSDKVKYDQGLVLGYEQKDLFKVETAFRSQKDTGKKLDKVEGVILPKDTEIKKGEYFKSVEGAHDNAKTDDVFDDAALVDPiPGKTDVKKLKATKAVFKRVMKDGDTNYWTDKYALGVYGEVKPIKDLRVAIGTAYVFGRLSGDkdvlkaVGDSDNRGDITFFTGADYKLSLLEKFVVNPVVTYTLYADAKWNGADEklyypeDLKTSMLKTGVRFGWGEEK---KSNSLLYDFFGKNTLVYDTNKEDKGDDKLLPGVSLFGAFDLVNKNIETKLPLMMTFYSGELVKGLNVAALVHANVAKDASEIsrvvpgtvYAGRMTKADYERLIGAKGLQIGLAASYDVKLND-ITIVPAAAMLWTHGMLKGeADTRMTADEFKVEAKVDVKGVIQNTTLSVFWDEAAFGKGTSKEWtfgvkHDEQNYYTLKNGVFGLKAKIAL
>tr|F4LK31|F4LK31_TREBD Uncharacterized protein OS=Treponema brennaborense (strain DSM 12168 / CIP 105900 / DD5/3) GN=Trebr_2078 PE=4 SV=1
AEPVADVKIAEFSGNASVQWGVNLDSGKTGFLNAYEVVFKLNLLNNGTKSTTGDGVWGELVLKTDDDTFIGWKNTENSDGkFNANKGMQDGKNLGLKVFVDVAKIHLGPAYIGIKRGDTQTGELKMDA-AIRSSDDDQ--AKWLSNVGPDKFSQGIVVGFAN-DMFGIDVDLRSYAVDK-----------------------------------------------------------------TDSTDIVNQYTGAYAFAGEAEFKGVENLSIKAGASYNFSDKFYAntasdtS--ASLDTVLGYSASAGYKLALNDTYYIRPQVGFAGANSKTDA----nnSKSGMAMAFGVLFGWGEIGMDKNADVAF--------------LDDDMAKKVSPGVGVVAYVPFKGTSKVagvssdaeqlYTARIMPSFFSGEIVKNLTAAAYGDIVVMNDKYPTv----A--------NKDMGMAFVLSAKYAIPV-DAMTITPNAGVRFANASYADnykdfgeaddgvfgkkdgtyklsmgdqktktGSALFDGNFMNIKAGVDVAGLISNTTLSVIYESANVLNSLEAA----SGANVSKLGTLNFKAKIAL
>tr|F4LK33|F4LK33_TREBD Autotransporter beta-domain protein OS=Treponema brennaborense (strain DSM 12168 / CIP 105900 / DD5/3) GN=Trebr_2080 PE=4 SV=1
AEPVADVKIAEFSGNASVQWGVNLDSGKTGFLNAYEVVFKLNLLNNGTKSTTGDGVWGELVLKTDGDTFIGWKNTSYGDTaTKSGEGMT--SDLKLKTFVDVAKIHLGPAYIGIKSGDTRTGSLKMDA-AIRSADNDNafipvvsnednKTYNYLHDVGPKGFSQGIVAGFAN-DMFGIDVDLRSYEA-------------------------------------------------------------------------TTQYSNAYAFAAEAEFKGVENLSVKAGASYNFSDKYYNddtssvK--TSLANVMGYSASAGYKLALNDTYYIRPQVGFTGTNSTQTVAS--vetKSNSMDMAFGVLFGWGEIGMDKNADVPF--------------LDNDGAKKVSPGVSIHAAMPLAAKTGDtdylkdgRAIVLRPAFFSGEIVKNLTVAALADIVLPV-GYDN-------------NPDPMFGMVFGVKYAIAV-DAITVTPNFGVRFANKEYAAyakavvaenneslitrdwydgtteknaAINGSVDGIMNIKAGVDVAGLISNTTLSLIYESANLQNSKDYT----GTANPVKLGTLNLKAKIAL