[maker-devel] Error from Pseudo gene identification scripts
Quanwei Zhang
qwzhang0601 at gmail.com
Mon Dec 11 09:47:30 MST 2017
Hi Nick:
Thank you Nick. It seems the error is really due to the sequence name. Now
"pseudo_wrap.py" is running after I change the names. But there are still
some things seem strange.
(1) I found in the file "log_step1", it shows below information at the top.
Does it matter?
NOTE: DatabaseOp not imported
NOTE: DatabaseOp not imported
...
(2) It also shows below information
Done!
sh:
/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/fasta36.3.8e/bin//tfasty34:
No such file or directory
sh:
/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/fasta36.3.8e/bin//tfasty34:
No such file or directory
sh:
/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/fasta36.3.8e/bin//tfasty34:
No such file or directory
....
While when I look into the folder
"/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/fasta36.3.8e/bin/", I found
there is no file "tfasty34". Instead, there is a file named "tfasty36".
fasta36 fastf36 fastm36 fasts36 fastx36 fasty36 ggsearch36
glsearch36 lalign36 map_db README ssearch36 tfastf36 tfastm36
tfasts36 tfastx36 tfasty36
Do you have any suggestions on this?
Best
Quanwei
2017-12-11 10:18 GMT-05:00 Quanwei Zhang <qwzhang0601 at gmail.com>:
> 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:Pseu
>> dogene>
>> >>>>
>> >>>> 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/s
>> cript_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_yand
>> ell-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=2GYyuVGmT
>> 8vENvvk0LPCHjSUEmEzXdcyOnhXDjoTEcQ&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=>
>> > --------------------------------------
>> >
>> >
>>
>>
>
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