Not able to translate long protein sequences to 3Di

[cheche0109]

My idea is when ProstT5 needs to predict/translate the protein sequence longer than around 500 amino acids long, it has very high chance of translating the 1D protein sequences to all d predictions which is nonsensical. When I was shortening a sequence to 480 amino acids long, the 3Di representation kinda makes sense.

python translate.py -i ./large_5.faa -o out --half 1 --is_3Di 0

Using device: cuda:0

Result directory already exists! - Watch out to not overwriting existing results!

is_3Di is False. (0=expect input to be AA, 1= input is 3Di

##########################

Loading model from: Rostlab/ProstT5

##########################

You are using the default legacy behaviour of the <class 'transformers.models.t5.tokenization_t5.T5Tokenizer'>. This is expected, and simply means that the legacy (previous) behavior will be used so nothing changes for you. If you want to use the new behaviour, set legacy=False. This should only be set if you understand what it means, and thoroughly read the reason why this was added as explained in huggingface/transformers#24565

##########################

Input is 3Di: False . Sequence below should be lower-case if input is 3Di.

Example sequence: >GUT_GENOME107594_03343

MDNDKRKKVYDVLTSKTGYKDSFDDFNKFMDDGAARRKVYDVLREQTGYRDSFEDFDKFMSSSHQGEMPVPIVPMRPTEPDLSFSNPSAGKFVQNGLDANEELLNDVKAEPVKDGMGRSYFPVKPQKVMEDEIRREYQVEPIESQINNAIVANEEAIRRIEQGKTEDYDRKAEEHPFLHALGGFARQHEGRVPDVNPSNDKEALRNLYAERNKLEEAKKVIEASRTDGILSNISAGVKDAVTDMGFYDFGMTEMSDNSRLLGIKAKLDNKQPLTEDEQKLLNAAALAQGVQSSHQDRISPWYTAGQTTANMAPFMAEMLVNPAAGLGKAAQKAVTKKVSGLVGKSLTRKMLPKLSRVAGDVAGASVMTGTTGIMRTVADAEGRMLGDVNSSIRDGEIVGNGFSGGLDAGEASAKAFGANTIENWSEMLGEYFAPALRGMGMVADKGMRKMGLGRVSDFISDINSTSLARGIDDFLEKTQWNGPIGEIAEEEAGIIANSYITGDNKLSDLTDPRLQLDIVLGVGLFGGFVSGMKTIGYRSPSKIAEKDLKRAEKNASSMFDNWEDIRLEIENTDEEQLPDTLNSIIGHAAGNDNAKKAAIVDYAYSLQKWRGVNAAKLKQTVENPAEAQNLVENEENGTGVEAIPEFDKVSVYRNFKRAERKVAQALPNTPIEKIEDVTDVDKFAADNGLNEEQKSAVTDYMAAKEPYSIYQSDVEARKEVVKSNAREQAVKDAERTSNPDTGFITQVKRKFSETPVYLVGGNLSFGDDGLLDRSNSTETVYYLDENGKRLPAPAEDFDSIVSQSSKEELVANAEAQATADFDAQENESLASPEILPPGIGETVSLDGGTYVIEGADNDNPGNFSALKLNTDGEIEVTPGLSEQISLSPDEYYEAKETELWKNDGIQPEQPVGKVDEVVAPALVQGVDKMPEISAENTSGPEMEDNKVSEETPEQRLQKVVDSLPKKKDGNIDYKALTPQQRFDYTSAAESPEVAIEDLKSDVAVKNEELEKINARLEKAIGGERVELRDTIRSKKKELDELTAFFQSVVPEQPDTSVNEEQPSVPEDVRTDEDYVEWVADNSDDAEEVLGAYSVAKELASHEQTLKPWQRELLGRKVSTSSFVRFGDRNHITGTLAKGWLRKDGEEIDSIAQELTANGVDVSEQDIVDFILDNPSNRVSEISDTMRSLSSRFSEIATKETGIPVGGPESNTGKLYIQLKEANKKIDELTDEQKADMRNALIADMDASDVQRSGDYYESLADYAEQYDRFRDEMNAEEADEAVIRQMEAESPTLYHGGFTADELDDIYSQIENDNGTERQTEDSGETQPALSGDEIEQREEPGIPDAVGAEDSESEGQDSGVVPDIEEIQDNTLDNEDESLSLHLNSKEEENGTISESVPQGERREETPQNGSLEEATDRLRERSRANEEARSRSGKTLSFQEKLAEEARETEAYAKEKGSWIPMSKVFDLGASGPSGNEADTYISQDNHIYKVNNLMNSKGILPLLERVALHNAIFPSSQYELTGFTGFEGGNVYPVLRQRYVPNATLSSPEEIDSYMRSLGFKQTGEAAYSNGDVVISDLRPRNVLKDTDGDLYVVDADFKKEDAVSFEASPISPGENVLDYAERISREKEMHDVRQSVDTNPTDAQKEAGNYKKGHIRLDGYDITIENPKGSERSGTDAKGGKWSVTMNNDYGYIRGTQGVDGDHIDVFLSDDPTTGNVYVIDQVKEDGSFDEHKVMYGFGSALAAKRAYLSNYSKGWNGLGKITQVSKDEFRKWVNSSRRKTKPFAEYKSVKMESDVRTDRQGNPVDADGKLIIEGNRLVTDKRYAELLERMRKKLGGQMNMGVDPEILAIGTEMAVYHIEKGARKFAEYAKAMIADLGDVIRPYLKSFYNGARDLPEMQELAKNMDSYNDVSSFDVVNFDKVIPDVINGIATMAEEKEIKRQADVANAAIKKVRSKNKKKNNNVSLPLGDLFNQNIEEYGKEQRKESDSGSEGNQGTNGQLGEGAWEEDRKSGLQGETGSVSGRDGADADRGGRVHGVSVGRQSSVKRNRNNYSFGDSHIDVPSGDVAKLKANVAAIRTLKEIEESGLPATDEQKAILAKYSGWGGLSNALNDEKYNARKSYYGADKNWNEKYLPYYEQLIELLTPEEFRSAVQSTTTSHYTPETVIRSMWDIAGRIGVKGGDVSEPAMGIGRIIGLMPDETSSRSRISGYEIDSLSGRISKALYPDANIKVQGYETEFFPQSKDLVITNVPFGKQAPYDKALEKTLKKQMKGAYNLHNYFIAKSLLELKEGGIGIFVTSSATMDGASSRFREFASSGGFDLVGAIRLPNDAFQKDAGTSVTADVLVFRRRKSGEKPNEINFISTTQIGEGNYQENGETRTKPIMVNEYFASHPEMMLGEMMTAYDAGSGGLYSGASQTLKAKPGMDLQKALDAAVKKLTENVNIGIENADSRLENTEKEQTTLKNGTLSVKDGKVYVAMNGVLEEIAVKDKFVYSGKTRKTADAVNEYNELKSTLRELISEEQKKGGNPEPLRKKLNEQYDGFVGKYGTLNRNKALDDVFDEDFEHNLPLSLETVRRVPSPTGKSMVYEVEKGKGILDKRVNYPVEEPTKADSVKDAINISRSYKGNIDIPYIARLTGKGEEEVTEEMLRDGSAYRDPLTGTLVDRATYLSGNVKSKLEDARAMAENDPAFDKNVADLEKVQPETIRFGDISYRLGTPWIPAQYINEFAENVLGISGVDVTYMPSLNEFVVGKHARISDFEKSGAIGTDRVGAIDLFAYAINQRKPKIYDEHTEYGPSGSIKVRTVNEAETQAAAEKIMEISDKFIEYIDGRKGIHRELERIYNDKYNNYVLKKYELPSFSHMEKDEDGKEKMVTHYPNSNTSISMREHQARAIQRSIEGSTLLAHQVGTGKTFTMITTAMEMRRLGLARKPMIV

##########################

Average sequence length: 2940 measured over 1 sequences

Parameters used for generation: {'do_sample': True, 'num_beams': 3, 'top_p': 0.95, 'temperature': 1.2, 'top_k': 6, 'repetition_penalty': 1.2}

Example generation for 0_GUT_GENOME107594_03343:

seqs[batch_idx]

ddpvvvvvvvvvvcvppvddddpvvvvvvvpdpvvvvvvvvvvcvppvddddpvvvvvvvvppddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddd

Translating 1 proteins with an avg. length of 2940 took 2.7[m] (164.3[s/protein])

Writing results ...

python translate.py -i ./large_5.faa -o out --half 1 --is_3Di 0

Using device: cuda:0

Result directory already exists! - Watch out to not overwriting existing results!

is_3Di is False. (0=expect input to be AA, 1= input is 3Di

##########################

Loading model from: Rostlab/ProstT5

##########################

You are using the default legacy behaviour of the <class 'transformers.models.t5.tokenization_t5.T5Tokenizer'>. This is expected, and simply means that the legacy (previous) behavior will be used so nothing changes for you. If you want to use the new behaviour, set legacy=False. This should only be set if you understand what it means, and thoroughly read the reason why this was added as explained in huggingface/transformers#24565

##########################

Input is 3Di: False . Sequence below should be lower-case if input is 3Di.

Example sequence: >GUT_GENOME107594_03343

MDNDKRKKVYDVLTSKTGYKDSFDDFNKFMDDGAARRKVYDVLREQTGYRDSFEDFDKFMSSSHQGEMPVPIVPMRPTEPDLSFSNPSAGKFVQNGLDANEELLNDVKAEPVKDGMGRSYFPVKPQKVMEDEIRREYQVEPIESQINNAIVANEEAIRRIEQGKTEDYDRKAEEHPFLHALGGFARQHEGRVPDVNPSNDKEALRNLYAERNKLEEAKKVIEASRTDGILSNISAGVKDAVTDMGFYDFGMTEMSDNSRLLGIKAKLDNKQPLTEDEQKLLNAAALAQGVQSSHQDRISPWYTAGQTTANMAPFMAEMLVNPAAGLGKAAQKAVTKKVSGLVGKSLTRKMLPKLSRVAGDVAGASVMTGTTGIMRTVADAEGRMLGDVNSSIRDGEIVGNGFSGGLDAGEASAKAFGANTIENWSEMLGEYFAPALRGMGMVADKGMRKMGLGRVSDFISDINSTSLARGIDDFLEKTQWNGPIGEIAEEEAGIIANSYITGDNKLSDLTDPRLQLDIVLGVGLFGGFVSGMKTIGYRSPSKIAEKDLKRAEKNASSMFDNWEDIRLEIENTDEEQLPDTLNSIIGHAAGNDNAKKAAIVDYAYSLQKWRGVNAAKLKQTVENPAEAQNLVENEENGTGVEAIPEFDKVSVYRNFKRAERKVAQALPNTPIEKIEDVTDVDKFAADNGLNEEQKSAVTDYMAAKEPYSIYQSDVEARKEVVKSNAREQAVKDAERTSNPDTGFITQVKRKFSETPVYLVGGNLSFGDDGLLDRSNSTETVYYLDENGKRLPAPAEDFDSIVSQSSKEELVANAEAQATADFDAQENESLASPEILPPGIGETVSLDGGTYVIEGADNDNPGNFSALKLNTDGEIEVTPGLSEQISLSPDEYYEAKETELW

##########################

Average sequence length: 900 measured over 1 sequences

Parameters used for generation: {'do_sample': True, 'num_beams': 3, 'top_p': 0.95, 'temperature': 1.2, 'top_k': 6, 'repetition_penalty': 1.2}

Example generation for 0_GUT_GENOME107594_03343:

seqs[batch_idx]

ddpvvlvvvvvvvcvppvddddsvvvvvcvvdpvslvvvvvvvcvvpvddddsvvvvvvvvvvpdddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddplvvlvvllvvlvvvlvvlvvvvvvvvvvvvpdddddddddddddddddddddddpvvsvvvnvvsvvvsvvsvvvsvvvvvvvpddlvvllvlllvvlcvvvvvddpppvvvvlvvllvvlvvcvvvvhdddpvsvvsvvvvvvvvvvvvvvvvpddpssvvsnvvnvcvvvvvvcvvdvppdddpvvvvvvvvvvvvpddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddd

Translating 1 proteins with an avg. length of 900 took 0.6[m] (33.7[s/protein])

Writing results ...

python translate.py -i ./large_5.faa -o out --half 1 --is_3Di 0

Using device: cuda:0

Result directory already exists! - Watch out to not overwriting existing results!

is_3Di is False. (0=expect input to be AA, 1= input is 3Di

##########################

Loading model from: Rostlab/ProstT5

##########################

You are using the default legacy behaviour of the <class 'transformers.models.t5.tokenization_t5.T5Tokenizer'>. This is expected, and simply means that the legacy (previous) behavior will be used so nothing changes for you. If you want to use the new behaviour, set legacy=False. This should only be set if you understand what it means, and thoroughly read the reason why this was added as explained in huggingface/transformers#24565

##########################

Input is 3Di: False . Sequence below should be lower-case if input is 3Di.

Example sequence: >GUT_GENOME107594_03343

MDNDKRKKVYDVLTSKTGYKDSFDDFNKFMDDGAARRKVYDVLREQTGYRDSFEDFDKFMSSSHQGEMPVPIVPMRPTEPDLSFSNPSAGKFVQNGLDANEELLNDVKAEPVKDGMGRSYFPVKPQKVMEDEIRREYQVEPIESQINNAIVANEEAIRRIEQGKTEDYDRKAEEHPFLHALGGFARQHEGRVPDVNPSNDKEALRNLYAERNKLEEAKKVIEASRTDGILSNISAGVKDAVTDMGFYDFGMTEMSDNSRLLGIKAKLDNKQPLTEDEQKLLNAAALAQGVQSSHQDRISPWYTAGQTTANMAPFMAEMLVNPAAGLGKAAQKAVTKKVSGLVGKSLTRKMLPKLSRVAGDVAGASVMTGTTGIMRTVADAEGRMLGDVNSSIRDGEIVGNGFSGGLDAGEASAKAFGANTIENWSEMLGEYFAPALRGMGMVADKGMRKMGLGRVSDFISDINSTSLARGIDDFLEKTQW

##########################

Average sequence length: 480 measured over 1 sequences

Parameters used for generation: {'do_sample': True, 'num_beams': 3, 'top_p': 0.95, 'temperature': 1.2, 'top_k': 6, 'repetition_penalty': 1.2}

Example generation for 0_GUT_GENOME107594_03343:

seqs[batch_idx]

ddpvvlvvvvvvvcvvpvddddsvvvvvcvvdpvslvvvvvvvcvvpvddddsvvvvvvvvvvpdddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddpvvvvvvvvvvppppdllvvlvvllvvlvvvlvvlvvvvvvvvvvvcvvcvpvvvvvvvvvvpppddppppvvvsvvvnvvsvvvsvlsvllsvlvvvlvpddlvvllvlllvllcvvvvvddpcllvllpdpllvvlvvcvvvvhdddpvsvssvssnvssvvsvvvvvvsddpssvvsnvcnvcvvvvvvcvvcvppppppvvvvvvvvvvvvpddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddd