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Protein structure comparison tools such as SSAP and SNAP
http://cath-tools.readthedocs.io
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Parsing error when using hmmscan results file #74

Closed mrztm closed 3 years ago

mrztm commented 3 years ago

Hi,

I am trying to analyse the attached file using cath-resolve-hits. It is a result from hmmscan version 3.3.2 (without the alignments). Invoking the command cath-resolve-hits --input-format hmmscan_out hmmscan_res.txt results in the following error message 2021-03-09 21:15:21.306957 [cath-resolve-hits|error ] Unable to parse/process resolve-hits input data file "HMMER_Full.txt" of format hmmscan_out. Error was: Failed to parse a number (of type unsigned int) from

Could it be that cath-resolve-hits is incompatible with hmmscan version3.3.2?

Many thanks for your help Thomas

hmmscan_res.txt

tonyelewis commented 3 years ago

Thank you for using cath-resolve-hits and for reporting this issue.

From an initial look, I think it's failing because it's expecting to see alignments in the output. Note that the header of that file includes # show alignments in output: no. Please can you try regenerating the hmmscan output with alignments included and report back? Thanks.

I will look to make the error message more helpful in that situation.

mrztm commented 3 years ago

Hi Tony,

I have generated the result file including the alignments, see attachment. Unfortunately, it still causes an error.

cath-resolve-hits --input-format hmmscan_out --summarise-to-file test_summary.txt hmmscan_wali.txt 2021-03-10 16:12:33.145799 [cath-resolve-hits|error ] Unable to parse/process resolve-hits input data file "test3.txt" of format hmmscan_out. Error was: Failed to parse a number (of type unsigned int) from CS

I am going to try older versions of hmmscan. I hope that helps to narrow down the issue.

Many thanks for the quick response Thomas

Dr Thomas Millat Senior Research Fellow Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC) [SBRC_Signature] Room B18 University of Nottingham Biodiscovery Institute The University of Nottingham University Park Nottingham NG7 2RD

t: +44(0)115 95 16827 e: thomas.millat@nottingham.ac.ukmailto:thomas.millat@nottingham.ac.uk w: www.sbrc-nottingham.ac.ukhttp://www.sbrc-nottingham.ac.uk/ @SbrcNottingham [BBSRC_EPSRC_signature]

Von: Tony E Lewis notifications@github.com Gesendet: Mittwoch, 10. März 2021 11:24 An: UCLOrengoGroup/cath-tools cath-tools@noreply.github.com Cc: Thomas Millat mrztm@exmail.nottingham.ac.uk; Author author@noreply.github.com Betreff: Re: [UCLOrengoGroup/cath-tools] Parsing error when using hmmscan results file (#74)

Thank you for using cath-resolve-hits and for reporting this issue.

From an initial look, I think it's failing because it's expecting to see alignments in the output. Note that the header of that file includes # show alignments in output: no. Please can you try regenerating the hmmscan output with alignments included and report back? Thanks.

I will look to make the error message more helpful in that situation.

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hmmscan :: search sequence(s) against a profile database

HMMER 3.3.2 (Nov 2020); http://hmmer.org/

Copyright (C) 2020 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

query sequence file: CLAU_0004.faa

target HMM database: /store/HMM_data/PFAM/Pfam-A

per-seq hits tabular output: HMMER_Table.txt

per-dom hits tabular output: HMMER_Domain.txt

pfam-style tabular hit output: HMMER_Pfam.txt

profile reporting threshold: E-value <= 0.01

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query: lcl CLAU_CLAU_0004 [L=324] Description: [product=Glyoxylate reductase] [location=1365..2339] [locus_tag=CLAU_0004] [protein_id=ALU34433.1] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description 
6.7e-59  198.2   0.0    9.1e-59  197.8   0.0    1.2  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
1.3e-25   89.6   0.1    1.6e-25   89.3   0.1    1.1  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
3.1e-06   26.9   1.0    1.1e-05   25.1   0.3    2.0  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
4.6e-06   27.0   0.4      1e-05   25.8   0.1    1.7  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
9.6e-06   25.8   0.2    2.2e-05   24.7   0.2    1.6  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
6.4e-05   23.6   0.1    0.00017   22.2   0.1    1.7  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
0.00053   20.1   0.1     0.0014   18.7   0.1    1.8  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase

Domain annotation for each model (and alignments):

2-Hacid_dh_C D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain

score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc

1 ! 197.8 0.0 3.5e-62 9.1e-59 2 178 .] 113 292 .. 112 292 .. 0.94

Alignments for each domain: == domain 1 score: 197.8 bits; conditional E-value: 3.5e-62 HHHHHHHTTHHHHHHHHHTTCC.....HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTEEECSHHH CS 2-Hacid_dh_C 2 alllallrrlaeadeevregew.....ssekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkeeeeeeelgveyvslee 87 +lll+l+ +++ ++++v+eg+w + + + el kt GiiG+G+IGqa+ k+++a+gmkv+ay+r+k++ e+++v+y++l++ lcl|CLAU_CLAU_0004 113 SLLLELTNHVSIHNKAVKEGQWneigeWCFWKKPLMELGSKTAGIIGYGKIGQATSKIVQAMGMKVLAYNRHKNKV--LESENVKYAELND 201 799*****76554334466777****8854..677789* PP

                     HHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGTCHHHHHSTTEEE-SS-T CS
    2-Hacid_dh_C  88 llaesDivslhlpltketrhlinaeelakmkkgavliNtaRGglvdeeaLleaLksgkiagaalDvfeeeplpedspllelpnviltPHia 178
                     ++++sD+++lh+plt+et+++in++++++mk+g++++N aRG+l+ ee+L+ aL+ gk+ gaalDv++ ep++++spll+++n+i+tPHi+

lcl|CLAU_CLAU_0004 202 VFEKSDVIFLHCPLTEETKGIINSKSIEHMKDGVIIVNNARGPLIVEEDLAHALNIGKVYGAALDVTSREPIEKESPLLKAENCIITPHIS 292 *****96 PP

2-Hacid_dh D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain

score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc

1 ! 89.3 0.1 6.1e-29 1.6e-25 15 132 .. 21 321 .. 4 323 .. 0.94

Alignments for each domain: == domain 1 score: 89.3 bits; conditional E-value: 6.1e-29 HHHTTE.EEEEES.....SSSHTCHHHGGTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHH CS xxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF 2-Hacid_dh 15 lkekgv.evevkd.....ellteelaekakdadalivrsntkvtaevLeklpkLkviaragvGvDnvDldaakerGilVtnvpgystesvA 99 l++ + +++v+d ++ + ++e+++da++++++++ ++++v++ +pkLk+ + +++G++ vD++a k+ G++Vtn+p+yst++vA lcl|CLAU_CLAU_0004 21 LEK--LgDLTVYDktifdNSNDDLIIERIRDAEVVFTNKTP-ISENVFKSCPKLKYLGVFATGYNVVDIKASKKFGVVVTNIPSYSTDAVA 108 455..335555555555377788999*9998.*** PP

                     HHH........................................................................................ CS
                     xxx........................................................................................ RF
      2-Hacid_dh 100 Elt........................................................................................ 102
                     +++

lcl|CLAU_CLAU_0004 109 QMAvsllleltnhvsihnkavkegqwneigewcfwkkplmelgsktagiigygkigqatskivqamgmkvlaynrhknkvlesenvkyael 199 *** PP

                     ........................................................................................... CS
                     ........................................................................................... RF
      2-Hacid_dh 103 ........................................................................................... 102

lcl|CLAU_CLAU_0004 200 ndvfeksdviflhcplteetkgiinsksiehmkdgviivnnargpliveedlahalnigkvygaaldvtsrepiekespllkaenciitph 290 *** PP

                     ..T-BHHHHHHHHHHHHHHHHHHHTTCCGTTB CS
                     ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      2-Hacid_dh 103 ..faTeeaqeriaeeaaenllkalkgespana 132
                       +a +e++er+  +a+enl+++l+g +p n+

lcl|CLAU_CLAU_0004 291 isWAAKETRERLLNIAVENLKNFLEG-NPINV 321 **.55555 PP

IlvN Acetohydroxy acid isomeroreductase, NADPH-binding domain

score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc

1 ? 0.1 0.0 0.2 5.3e+02 47 80 .. 79 111 .. 43 127 .. 0.67 2 ! 25.1 0.3 4.3e-09 1.1e-05 2 92 .. 150 238 .. 149 260 .. 0.83

Alignments for each domain: == domain 1 score: 0.1 bits; conditional E-value: 0.2 TT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHH CS IlvN 47 egfevltvaeavkkadvvmiliPDelqkevyeee 80 +g++v++++ a+kk vv++ iP ++v + + lcl|CLAU_CLAU_0004 79 TGYNVVDIK-ASKKFGVVVTNIPSYSTDAVAQMA 111 445555543.445555555555555555555555 PP

== domain 2 score: 25.1 bits; conditional E-value: 4.3e-09 HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-.HHHHHHHHHHHTGGG--TT-EE CS IlvN 2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliP.Delqkevyeeeiepnlkegkal 91 l +k+ +iGyG G+a ++ ++ g++v +r+++ k ++e+++ ++++++ +k+dv+++ P e k +++++ +++k+g ++ lcl|CLAU_CLAU_0004 150 LGSKTAGIIGYGKIGQATSKIVQAMGMKVLAYNRHKN---KVLESENVKYAELNDVFEKSDVIFLHCPlTEETKGIINSKSIEHMKDGVII 237 568999****98888877...56678999943556678888888899999865 PP

                     E CS
            IlvN  92 a 92 
                     +

lcl|CLAU_CLAU_0004 238 V 238 4 PP

NAD_binding_2 NAD binding domain of 6-phosphogluconate dehydrogenase

score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc

1 ? -2.2 0.0 1.6 4.2e+03 11 45 .. 80 114 .. 73 126 .. 0.69 2 ! 25.8 0.1 4e-09 1e-05 3 89 .. 156 240 .. 154 256 .. 0.89

Alignments for each domain: == domain 1 score: -2.2 bits; conditional E-value: 1.6 HHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE CS NAD_binding_2 11 Gsnmarnllkagykvavydrtkekveelvaegaka 45 G n + +++++ v+v + + +++++++ +++ lcl|CLAU_CLAU_0004 80 GYNVVDIKASKKFGVVVTNIPSYSTDAVAQMAVSL 114 56666666778888888888877777777766544 PP

== domain 2 score: 25.8 bits; conditional E-value: 4e-09 EEEE-SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEEESSHHHHHHCBSEEEE-SSSHHHHHHHHHC.HCCC--TT-EEEE- CS NAD_binding_2 3 gfiGlGvMGsnmarnllkagykvavydrtkekveelvaegakaaesieelvasldvvilmvkagkavdevieg.llealekgdilidg 89 g+iG G+ G+ + +++ g+kv +y+r+k+kv +++ + ++++++++++ dv++l + +++++ +i++ +e+++ g i+++ lcl|CLAU_CLAU_0004 156 GIIGYGKIGQATSKIVQAMGMKVLAYNRHKNKVL---ESENVKYAELNDVFEKSDVIFLHCPLTEETKGIINSkSIEHMKDGVIIVNN 240 99***87764...45556778999****9999**999975 PP

AdoHcyase_NAD S-adenosyl-L-homocysteine hydrolase, NAD binding domain

score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc

1 ! 24.7 0.2 8.3e-09 2.2e-05 21 108 .. 150 239 .. 146 260 .. 0.85

Alignments for each domain: == domain 1 score: 24.7 bits; conditional E-value: 8.3e-09 -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEE.E...-SSSSSSB-HHHHCCS-TTEEEE CS AdoHcyase_NAD 21 iaGkvavvaGyGdvGkGcaaslkglGarvivteidPinalqaameGfevvtleevvkkadifv.t...ttGnkdiitvehlkkmkedaivc 107 ++ k+a ++GyG +G+ +++ ++++G +v+ + l + e + ++l++v +k+d++ t +k ii+++ +++mk+ i+ lcl|CLAU_CLAU_0004 150 LGSKTAGIIGYGKIGQATSKIVQAMGMKVLAYNRHKNKVLES--ENVKYAELNDVFEKSDVIFlHcplTEETKGIINSKSIEHMKDGVIIV 238 6889***99998888876..778889**86523222456899**998 PP

                     E CS
   AdoHcyase_NAD 108 n 108
                     n

lcl|CLAU_CLAU_0004 239 N 239 8 PP

F420_oxidored NADP oxidoreductase coenzyme F420-dependent

score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc

1 ! 22.2 0.1 6.4e-08 0.00017 3 73 .. 156 217 .. 154 242 .. 0.77

Alignments for each domain: == domain 1 score: 22.2 bits; conditional E-value: 6.4e-08 EEETTSHHHHHHHHHHHHTTS.GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHH CS F420_oxidored 3 aiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavsneeaaeeadvvvlavkpea 73 +iiG+G++g+a + ++a g +++ a +r+++k+ e ++ + + ++++e++dv++l ++ ++ lcl|CLAU_CLAU_0004 156 GIIGYGKIGQATSKIVQAMG---MKVL-AYNRHKNKVLESENV-----KYAELNDVFEKSDVIFLHCPLTE 217 9***....989999988665433.....3345899****9854 PP

Shikimate_DH Shikimate / quinate 5-dehydrogenase

score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc

1 ! 18.7 0.1 5.4e-07 0.0014 8 99 .. 148 232 .. 143 266 .. 0.83

Alignments for each domain: == domain 1 score: 18.7 bits; conditional E-value: 5.4e-07 S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-...SSSSS-SB-HHHH CS Shikimate_DH 8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisa...taseepilekeev 95 +l +k++ +iG G++++ + k a g+k v+ NR +++ e +e +k+ el+++ +++dv++ t ++ i++++++ lcl|CLAU_CLAU_0004 148 MELGSKTAGIIGYGKIGQATSKIVQAMGMK-VLAYNRHKNKVLE------SE---NVKYAELNDVFEKSDVIFLHcplTEETKGIINSKSI 228 578899*****9.999*9988754......22...45778888889**9743447788889999888 PP

                     HCCH CS
    Shikimate_DH  96 eeal 99 
                     e+++

lcl|CLAU_CLAU_0004 229 EHMK 232 8776 PP

Internal pipeline statistics summary:

Query sequence(s): 1 (324 residues searched) Target model(s): 18259 (3090017 nodes) Passed MSV filter: 626 (0.0342845); expected 365.2 (0.02) Passed bias filter: 489 (0.0267813); expected 365.2 (0.02) Passed Vit filter: 49 (0.00268361); expected 18.3 (0.001) Passed Fwd filter: 10 (0.000547675); expected 0.2 (1e-05) Initial search space (Z): 18259 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold]

CPU time: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.40

Mc/sec: 2467.14

// [ok]

tonyelewis commented 3 years ago

Thanks for your reply.

This appears to be an issue with the file containing 'CS' records (which look like they're probably secondary structure predictions) that cath-resolve-hits wasn't expecting.

I've just pushed a fix for that.

mrztm commented 3 years ago

Hi Tony,

Many thanks for the quick response. The new version runs smoothly over the file.

Kind regards Thomas

Dr Thomas Millat Senior Research Fellow Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC) [SBRC_Signature] Room B18 University of Nottingham Biodiscovery Institute The University of Nottingham University Park Nottingham NG7 2RD

t: +44(0)115 95 16827 e: @.**@.> w: www.sbrc-nottingham.ac.ukhttp://www.sbrc-nottingham.ac.uk/ @SbrcNottingham [BBSRC_EPSRC_signature]

Von: Tony E Lewis @.> Gesendet: Mittwoch, 10. März 2021 16:59 An: UCLOrengoGroup/cath-tools @.> Cc: Thomas Millat @.>; Author @.> Betreff: Re: [UCLOrengoGroup/cath-tools] Parsing error when using hmmscan results file (#74)

Thanks for your reply.

This appears to be an issue with the file containing 'CS' records (which look like they're probably secondary structure predictions) that cath-resolve-hits wasn't expecting.

I've just pushed a fix for that.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/UCLOrengoGroup/cath-tools/issues/74#issuecomment-795738428, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKXVJSVRAPEVINW73TFTLX3TC6QOVANCNFSM4Y4QH4OQ.

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tonyelewis commented 3 years ago

That's good to hear. Thanks for taking the time to report.

tonyelewis commented 3 years ago

@mrztm In case it's of relevance to you, we've brought the build back up and you can now download the latest executables from: here.

(The Mac executables currently depend on a brew install of icu4c but we'll look to address that.)