Can't see a way to attach the file, so I'll copy-paste it in as a separate comment - here it comes

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

HMMER 3.1b2 (February 2015); http://hmmer.org/

Copyright (C) 2015 Howard Hughes Medical Institute.

Freely distributed under the GNU General Public License (GPLv3).

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query HMM file: /home/jayoung/FH_fast_storage/repeats/getFullLengthElementsFromGenomes/getORF1referenceAlignment/alignment/ORF1align4.edit.fa.hmm

target sequence database: chr2_178837800-178843817_+_.fa.peps.fasta

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Query: ORF1aln4 [M=340]
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.2e-128 416.5 23.3 1.2e-128 416.5 23.3 2.4 2 chr2:178837800-178843817(+).fr1pep

Domain annotation for each sequence (and alignments):

chr2:178837800-178843817(+).fr1pep

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

---

1 ! 416.5 23.3 4.1e-129 1.2e-128 1 339 [. 303 637 .. 303 638 .. 0.98
2 ? 0.0 12.5 0.019 0.056 36 137 .. 942 1054 .. 918 1094 .. 0.49

Alignments for each domain:
== domain 1 score: 416.5 bits; conditional E-value: 4.1e-129
ORF1aln4 1 mgkkqrkksentkkqekspekkeqksspeeeekikeeeilelseeefkkiilkllkeleeelekekkevieklee 75
mgkkq++k++n+k+q++sp+ ke++ssp++e++++e++++el+ee f++ ++++el+e+++++ kev e+ e+
chr2:178837800-178843817(+).fr1pep 303 MGKKQNRKTGNSKTQSASPPPKERSSSPATEQSWMENDFDELREEGFRR---SNYSELREDIQTKGKEV-ENFEK 373
99**********************************************...78889999999999998.8999 PP

                        ORF1aln4  76 kleklekeieeiekklkelkeikkkieeikneleslknrieelEerisdledkleeikeeekesekrikkneesl 150
                                     +le++ ++i+++ek+lkel+e+k+k++e+++e++sl++r+++lEer+s++ed+++e+k+e k +ek+ik+ne+sl

chr2:178837800-178843817(+).fr1pep 374 NLEECITRITNTEKCLKELMELKTKARELREECRSLRSRCDQLEERVSAMEDEMNEMKREGKFREKIIKRNEQSL 448
*************************************************************************97 PP

                        ORF1aln4 151 .relsdtikrnNlriiGvpEeeeekekglenileeilkenFPnlkkeeeiqiqeaqRtPnrlnqkrktpRHiivk 224
                                        ++d++kr+Nlr+iGvpE++ e+ ++len+l++i++enFPnl++++++qiqe+qRtP+r++++r+tpRHiiv+

chr2:178837800-178843817(+).fr1pep 449 E-IWDYVKRPNLRLIGVPESDVENGTKLENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSRRATPRHIIVR 522
77.9********************************************************************** PP

                        ORF1aln4 225 ltkvkeKekiLkaarekkqvtykGkpirltaDlSaetlqarreWsdifqvLkeknlqPRilYPakLSfkidgeik 299
                                     +tkv++Kek+L+aarek++vt+kGkpirltaDlSaetlqarreW +if++Lkekn+qPRi YPakLSf ++geik

chr2:178837800-178843817(+).fr1pep 523 FTKVEMKEKMLRAAREKGRVTLKGKPIRLTADLSAETLQARREWGPIFNILKEKNFQPRISYPAKLSFISEGEIK 597
*************************************************************************** PP

                        ORF1aln4 300 vFtdkqkLkefvktkPaLqeiLkdalqeeeqnsakkkkrk 339
                                     +F dkq+L++fv+t+PaL+e+Lk+al++e++n+++  +++

chr2:178837800-178843817(+).fr1pep 598 YFIDKQMLRDFVTTRPALKELLKEALNMERNNRYQPLQNH 637
**********************************999886 PP

== domain 2 score: 0.0 bits; conditional E-value: 0.019
ORF1aln4 36 eeeilelseeefkkiilkllkeleeelekekkeviekl.........eekleklekeieeiekklkelke..i 97
++++ + ++ fk ++ ++ l+ ++k++++ i +l +e++++ ++ +ei+k +elke +
chr2:178837800-178843817(+).fr1pep 942 KDTTYQNLWDAFKAVCRGKFIALNAYKRKQERSKIDTLtsqlkelekQEQTHSKASRRQEITKIRAELKEieT 1014
4445555566777777777777774444444444444411111111122222222223333333333333333 PP

                        ORF1aln4   98 kkkieeikneleslknrieelEerisdledkleeikeeek 137 
                                      +k+++ i+++ + + +ri++++  ++ l +k  e+++  +

chr2:178837800-178843817(+).fr1pep 1015 QKTLQKINESRSWFFERINKIDRPLARLIKKKREKNQIDT 1054
4444444444444445555554444444444444333332 PP

Internal pipeline statistics summary:

Query model(s): 1 (340 nodes)
Target sequences: 3 (6015 residues searched)
Passed MSV filter: 1 (0.333333); expected 0.1 (0.02)
Passed bias filter: 1 (0.333333); expected 0.1 (0.02)
Passed Vit filter: 1 (0.333333); expected 0.0 (0.001)
Passed Fwd filter: 1 (0.333333); expected 0.0 (1e-05)
Initial search space (Z): 3 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]

CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01

Mc/sec: 204.51

//
[ok]

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Does your patch pass all the bioperl tests? If so, create a pull request.

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I don't have a patch - just a bug report. Sorry!

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Hi Janet,

Can you try to attach the file again? I think this is a new github feature that may not have been available before. That would make it easier to reproduce the error than trying to copy the above report.

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Hi there,

Sorry it took me a month to get back to you on this. I just tried attaching the file, but no luck: "Attaching documents requires write permission to this repository. Try again with a PNG, GIF, or JPG." It's a plain text file (before I added .txt to my non-standard name, I got a different error, that the file type was not supported). I'm happy to email the file to whoever wants it, or maybe someone can get me write permission?

thanks,

Janet

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@jayoung maybe post the file as a gist

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https://gist.github.com/jayoung/f7230a83410518d0bc24#file-gistfile1-txt

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Thanks, @pcantalupo - I think that worked.

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closing based on Francisco's fix in b5e68c7

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Oh, I didn't realize that we stumbled on the same bug. Thanks for closing Paul!

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Thanks for the fix - much appreciated.

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