[maker-devel] Error from Pseudo gene identification scripts

Quanwei Zhang qwzhang0601 at gmail.com
Mon Dec 11 08:18:02 MST 2017 

Thank you Nick. The output is shown below.

Traceback (most recent call last):
  File
"/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py",
line 4330, in <module>
    parse.get_qualified4(blast,fasta,E,I,L,P,Q)
  File
"/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py",
line 3050, in get_qualified4
    N = sizes[L[0]]
KeyError: 'maker-Contig2656-snap-gene-1.9-mRNA-1'
Traceback (most recent call last):
  File
"/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg/script_step3b.py",
line 98, in <module>
    oup.write("%s\t%s\t%s\t%s\n" % (all_contigs[i][0][0],
IndexError: list index out of range
Done!

NOTE: DatabaseOp not imported
Program  : tfasty34
Pair list: ../maker2.blastn.m_parsed_G500.PE_I500.PS1.pairs
Fasta1   : ../../prediction2_final.proteins.fasta
Fasta2   : ../maker2.blastn.m_parsed_G500.PE_I500.PS1.subj_coord.fa
Fasta dir: /gs/gsfs0/users/qzhang/tools/maker2_pseudogene/fasta36.3.8e/bin/
Working d:
Flags    : -A -m 3 -q
E thres  : 1.0
Read gene pairs...
 0 pairs
Read fasta files...
Do sw...
Done!
Read BLOSUM50 matrix...
Read the sw.out file...
Compare sequences:
 total: 0 alignments
Done!
Check parameter file...
 default: ml_t=30
 default: ev_t=5
 default: ml_p=0.05
 default: id_t=40
Filter ../maker2.blastn.m...
 E:5 I:40 L:30 P:0.05
Get pseudoexons...
 pseudoexon file: ../maker2.blastn.m_parsed_G500.PE
Get phase 1 pseudogene...
 phase1 ps file: ../maker2.blastn.m_parsed_G500.PE_I500.PS1
Get pair file and subject coordinates...
 pair file  : ../maker2.blastn.m_parsed_G500.PE_I500.PS1.pairs
 coordinates: ../maker2.blastn.m_parsed_G500.PE_I500.PS1.subj_coord
Get phase 1 pseudogene sequences...
 phase 1 ps sequence:
../maker2.blastn.m_parsed_G500.PE_I500.PS1.subj_coord.fa
Find stop and framshifts...
 Smith-Waterman outputs:
../maker2.blastn.m_parsed_G500.PE_I500.PS1_pairs.sw.*
 Final output:
../maker2.blastn.m_parsed_G500.PE_I500.PS1_pairs.sw.out.disable_count

The pseudogene pipeline has finished!


Best
Quanwei

2017-12-11 10:01 GMT-05:00 <panchyni at msu.edu>:

> Quanwei, in addition to checking the sequence file, can you also send
> me the standard output of the run (this the text that normally prints
> to the terminal unless you pipe it somewhere else)? This would help
> in diagnosing the problem, but Shin-Han is likely correct that it is an
> issue in the name formatting.
>
> Nick
>
> Quoting Shin-Han Shiu <shius at msu.edu>:
>
> > Hi Mike and Carson, we will take over from here. Thanks for referring
> > the message to us.
> >
> > Quanwei, it looks like for some reason your input sequence file is
> > missing "maker-Contig2656-snap-gene-1.9-mRNA-1". This can be an issue
> > with the sequence name since the code use space as delimiter in
> > places. Can you check your sequence file for this sequence and let us
> > know how the name after ">" look like?
> >
> > Nick, sorry for bugging you. Do you have any input on this?
> >
> > Shinhan
> >
> >
> > On 12/10/2017 8:37 PM, Michael Campbell wrote:
> >> Hi Quanwei,
> >>
> >> My guess would be a file format issue, but the code has evolved
> >> since I worked with it. The last time that ran it the fasta header
> >> had to contain only the sequence ID without a space after it. That
> >> was the big gotcha that I remember.
> >>
> >> I?ve ccd Shin-Han Shiu on this one. The pipeline was developed in his
> lab.
> >>
> >> Thanks,
> >> Mike
> >>
> >> On Dec 8, 2017, at 8:46 AM, Quanwei Zhang <qwzhang0601 at gmail.com
> >> <mailto:qwzhang0601 at gmail.com>> wrote:
> >>
> >>> Thank you Carson and Michael.
> >>>
> >>> Best
> >>> Quanwei
> >>>
> >>> 2017-12-07 23:42 GMT-05:00 Carson Holt <carsonhh at gmail.com
> >>> <mailto:carsonhh at gmail.com>>:
> >>>
> >>>    I?m going to CC Michael Campbell on this. I wasn?t really
> >>>    involved with any of the pseudogene accessory scripts and
> >>>    protocols that went with the MAKER-P publication nor have I
> >>>    really been involved with pseudogene annotation in general. So
> >>>    Michael might have more insight here.
> >>>
> >>>    ?Carson
> >>>
> >>>>    On Dec 7, 2017, at 2:44 PM, Quanwei Zhang <qwzhang0601 at gmail.com
> >>>>    <mailto:qwzhang0601 at gmail.com>> wrote:
> >>>>
> >>>>    Hello:
> >>>>
> >>>>    I am trying to identify pseudo genes following
> >>>>    http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene
> >>>>    <http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene
> >
> >>>>
> >>>>    After I get the blast result, I am trying to scan pseudogenes by
> >>>>    the command "python pseudo_wrap.py parameter". But I got the
> >>>>    following errors. Do you have any ideas and suggestions about
> >>>>    the errors? Thanks.
> >>>>
> >>>>    ##below shows reported errors
> >>>>    Traceback (most recent call last):
> >>>>      File
> >>>>
> >>>> "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//
> ParseBlast.py",
> >>>>    line 4330, in <module>
> >>>>        parse.get_qualified4(blast,fasta,E,I,L,P,Q)
> >>>>      File
> >>>>
> >>>> "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//
> ParseBlast.py",
> >>>>    line 3050, in get_qualified4
> >>>>        N = sizes[L[0]]
> >>>>    KeyError: 'maker-Contig2656-snap-gene-1.9-mRNA-1'
> >>>>    Traceback (most recent call last):
> >>>>      File
> >>>>
> >>>> "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg/
> script_step3b.py",
> >>>>    line 98, in <module>
> >>>>        oup.write("%s\t%s\t%s\t%s\n" % (all_contigs[i][0][0],
> >>>>    IndexError: list index out of range
> >>>>    Done!
> >>>>
> >>>>    Best
> >>>>    Quanwei
> >>>>    _______________________________________________
> >>>>    maker-devel mailing list
> >>>>    maker-devel at box290.bluehost.com
> >>>>    <mailto:maker-devel at box290.bluehost.com>
> >>>>    http://box290.bluehost.com/mailman/listinfo/maker-devel_
> yandell-lab.org
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMCAw&c=nE__W8dFE-shTxStwXtp0A&r=amxxAQj1r58HtnljR_ldsiP-fOO39FxiO68ZT1UBHoE&m=p2cRRr06c6fbtMo9iCwpKi0X1QnRoogK33tX5Bfd5ek&s=SeSN1OfBVQVhi5forovCTfSJGCO1bR7Q7LuCcWlhctI&e=>
> >>>>
> >>>> <https://urldefense.proofpoint.com/v2/url?u=http-
> 3A__box290.bluehost.com_mailman_listinfo_maker-
> 2Ddevel-5Fyandell-2Dlab.org&d=DwMFaQ&c=nE__W8dFE-shTxStwXtp0A&r=
> rf2UnAHeUSb4ulp2JbXt_w&m=4eCUx-nUmZ43poIB8geM9XkIKXoND4Yzi4aw4bXAfUU&s=
> 2GYyuVGmT8vENvvk0LPCHjSUEmEzXdcyOnhXDjoTEcQ&e=>
> >>>
> >>>
> >
> > --
> > --------------------------------------
> > Shin-Han Shiu
> > Michigan State University
> > Department of Plant Biology
> > 2265 Mol Plant Sci Bldg
> > (TEL) +1-517-353-7196 <(517)%20353-7196>
> > http://goo.gl/keiHZX
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_keiHZX&d=DwMCAw&c=nE__W8dFE-shTxStwXtp0A&r=amxxAQj1r58HtnljR_ldsiP-fOO39FxiO68ZT1UBHoE&m=p2cRRr06c6fbtMo9iCwpKi0X1QnRoogK33tX5Bfd5ek&s=pk3W0L_Z0dlNJDAdwrb7dA0_NSdr21LVNthDV6V43qg&e=>
> > --------------------------------------
> >
> >
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20171211/2376a128/attachment-0003.html>

More information about the maker-devel mailing list