Zhanglab forum

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

Dear user,

Can you post your a3m file as an attachment?

Best
IT Team

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

Hi,

Such error happens when CCMpred did not run successfully. You can check the following:

1. Check if CCMpred have the exe permission
2. Check if CCMpred can run successfully, for example, check the stdout file generated by CCMpred. If the output file does not contain anything or there are some error information in it, you can re-compile CCMPred and replace the built-in one.

If you still have problems, please just let me know.

Thanks,
Yang Li