WARNING message in phylosift

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mkniz...@gmail.com

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Jun 20, 2017, 8:33:32 PM6/20/17
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Good day,

My name is Nizam. I am running phylosift to check for the completeness of our bacterial draft genomes. Previously, all my runs were successful. However, recently I came across a warning message like this:

--------------------- WARNING ---------------------

,SG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is 

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


------------- EXCEPTION: Bio::Root::Exception -------------

GGAAGAGAGCA] which does not look healthyAATCGTACCGCCAAGGAAGTTC

STACK: Error::throw

STACK: Bio::Root::Root::throw /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/Bio/Root/Root.pm:472

STACK: Bio::PrimarySeq::seq /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/Bio/PrimarySeq.pm:285

STACK: Bio::PrimarySeq::new /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/Bio/PrimarySeq.pm:239

STACK: Bio::LocatableSeq::new /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/Bio/LocatableSeq.pm:121

STACK: Phylosift::FastSearch::translate_frame /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/Phylosift/FastSearch.pm:733

STACK: Phylosift::FastSearch::write_candidates /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/Phylosift/FastSearch.pm:1053

STACK: Phylosift::FastSearch::launch_searches /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/Phylosift/FastSearch.pm:319

STACK: Phylosift::FastSearch::run_search /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/Phylosift/FastSearch.pm:136

STACK: Phylosift::Phylosift::run_search /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/Phylosift/Phylosift.pm:418

STACK: Phylosift::Phylosift::run /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/Phylosift/Phylosift.pm:175

STACK: Phylosift::Command::search::execute /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/Phylosift/Command/search.pm:54

STACK: App::Cmd::execute_command /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/App/Cmd.pm:243

STACK: App::Cmd::run /Users/umdp/Desktop/phylosift_v1.0.1/bin/../lib/App/Cmd.pm:171

STACK: /Users/umdp/Desktop/phylosift_v1.0.1/bin/phylosift:7

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


May I know what could have gone wrong and how can I fix this?many thanks!


Best Wishes,


Nizam

Guillaume Jospin

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Jun 20, 2017, 8:43:47 PM6/20/17
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Looks like you have a ] character in your sequence. 

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mkniz...@gmail.com

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Jun 21, 2017, 4:23:00 AM6/21/17
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When I searched the following sequence (GGAAGAGAGCA]) in my contig file, I could not located the ] character (see attachment)
Troubleshoot 1.jpg

Guillaume Jospin

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Jun 21, 2017, 10:00:38 AM6/21/17
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Hrm, wold you be willing to send me your input file if it's not too large and I can see if there is something strange happening?


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mkniz...@gmail.com

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Jun 21, 2017, 8:08:43 PM6/21/17
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This is my input file. Thanks for your kind help :)


On Wednesday, 21 June 2017 08:33:32 UTC+8, mkniz...@gmail.com wrote:
BRC7-11.fna

Guillaume Jospin

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Jun 21, 2017, 8:43:17 PM6/21/17
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So as you mention, I couldn't find the ] character either.
I did a bit more digging and was able to reproduce your error.

I modified your input file using the following command:

perl -pi -e 's/\r//g' BRC7-11.fna

And things seem to work better now.

This command removes the extra return character that Macs tend to add at the end of lines. I guess BioPerl does not like them.

Let me know if this works out for you.

Guillaume


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mkniz...@gmail.com

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Jun 21, 2017, 11:48:14 PM6/21/17
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Yes, the command worked and I can successfully run phylosift on all my samples now. Thanks so much for your kind help. I really appreciate it :)


On Wednesday, 21 June 2017 08:33:32 UTC+8, mkniz...@gmail.com wrote:
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