autoAug.pl error

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katharina
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autoAug.pl error

Post by katharina »

Originally posted in the old forum by willj on 25.07.2013 - 05:00
Hi guys,
I am trying to run autoAug.pl, but am getting an error:
2 checking for installed programs ... ok.
1 Checking fasta headers in file /work/will/genome/bin/augustus/APLG_003_scaff.fasta.masked...
1 Checking fasta headers in file /work/will/genome/bin/augustus/GG_Trinity_PASA_clean.fasta...
3 mkdir gbrowse
3 mkdir pasa
3 mkdir training
2 All necessary directories have been created unter /work/will/genome/bin/augustus/autoAug/trainingSet.
3 cd /work/will/genome/bin/augustus/autoAug/seq
3 Cleaning genome file from DOS whitespaces/linebreaks...
3 perl /home/will/devel/bioinfo/augustus.2.7/config/../scripts/cleanDOSfasta.pl /work/will/genome/bin/augustus/APLG_003_scaff.fasta.masked > /work/will/genome/bin/augustus/autoAug/seq/genome_clean.fa
1 ####### Step 0: Creating training set with genes using PASA #######
3 cd /work/will/genome/bin/augustus/autoAug/trainingSet/pasa
2 Skipping seqclean. Using existing transcripts.fasta.clean.
2 Using existing alignAssembly.config.
3 ln -fs /work/will/genome/bin/augustus/autoAug/seq/genome_clean.fa genome.fasta
3 Reading MySQL variables from /home/will/devel/bioinfo/PASA/PASA2/pasa_conf/
1 Dropping MySQL database PASAmygenome on host gdudev.anu.edu.au.
2 Executing the Alignment Assembly: perl /home/will/devel/bioinfo/PASA/PASA2/scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g /work/will/genome/bin/augustus/autoAug/seq/genome_clean.fa -t transcripts.fasta.clean -T -u transcripts.fasta 1>Launch_PASA_pipeline.stdout 2>Launch_PASA_pipeline.stderr ...2 A test output...
Failed to execute, possible reasons could be:
1. There is already a database named "PASAmygenome" in your mysql host.
2. The software "slclust" is not installed correctly, try to install it again (see the details in the PASA documentation).
3. The fasta headers in cDNA or genome file were not unique.
Inspect /work/will/genome/bin/augustus/autoAug/trainingSet/pasa/Launch_PASA_pipeline.stderr for PASA error messages.
The error I get in Launch_PASA_pipeline.stderr looks like this:
Error, must specify at least one primary aligner via --ALIGNER or imported via --IMPORT... at /home/will/devel/bioinfo/PASA/PASA2/scripts/Launch_PASA_pipeline.pl line 311.
Whereabouts do I specify --ALIGNER?
Thanks very much
Cheers
Will
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Re: autoAug.pl error

Post by katharina »

by katharina on 25.07.2013 - 12:15
Which version of PASA have you installed?
We run autoAug.pl with PASA Version Jan-09-2011. Maybe the call for Launch_PASA_pipeline.pl has changed since then?
Instead of installing an older PASA version, you can also try to simply modify the PASA calls in the autoAug scripts (the usage of the argument ALIGNERS is explained at http://pasa.sourceforge.net/#A_sii). I don't know whether anything else changed in PASA, though (i.e. output file names, file formats... that would also cause problems).
Katharina
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Re: autoAug.pl error

Post by katharina »

by willj on 26.07.2013 - 00:28
Hi Katharina,
Thanks for getting back to me so quickly. I managed to modify autoAug.pl to get the --pasa option to run correctly. I inserted
--ALIGNER blat
at line 442 of autoAug.pl.
Thanks for your help
Will
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Re: autoAug.pl error

Post by katharina »

by willj on 26.07.2013 - 04:43
Hi Katharina,
I am using Stable Release PASA2-r20130605
I found another bug in autoAug.pl with --pasa turned on. At line 461 of autoAug.pl I had to include the options
--pasa_transcripts_fasta mydb.assemblies.fasta
and --pasa_transcripts_gff3 mydb.pasa_assemblies.gff3 as these are the inputs for $PASAHOME/scripts/pasa_asmbls_to_training_set.dbi.
I ran into another problem when mydb.assemblies.fasta.transdecoder.cds was not renamed as trainingSetCandidates.cds so I renamed it.
Do you think these problems are due to me using the most recent PASA?
Thanks
Will
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Re: autoAug.pl error

Post by katharina »

by katharina on 29.07.2013 - 10:17
Well, yes, but we intend to adapt the autoAug.pl pipeline to the new PASA. It might still take us some time, though.
Thank you for pointing out how you fixed the problems. That information will be very useful for others who already work with the newer PASA.
Katharina
Best,
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Re: autoAug.pl error

Post by katharina »

by Kevin K. on 02.06.2014 - 06:43
New version of autoAug.pl available?
Hi Katharina,
Just following up on this issue. I'm having trouble getting autoAug.pl (the one bundled with augustus-3.0.2) to work with PASA (PASA_r20140417). I had to add the --ALIGNERS flag as mentioned above but I'm still having trouble beyond that.
1 ####### Step 0: Creating training set with genes using PASA #######
3 cd /media/kmkocot/Sclerite/MAKER/Cephalodiscus_hodgsoni_training_set/autoAug/trainingSet/pasa
Warning: missing.
2 Running perl /usr/local/bin/PASA_r20140417/seqclean/seqclean/seqclean transcripts.fasta 1>seqclean.stdout 2>seqclean.stderr ... Finished!
3 cp /usr/local/bin/PASA_r20140417/pasa_conf/pasa.alignAssembly.Template.txt alignAssembly.config
3 Setting appropriate values in alignAssembly.config
3 rm alignAssembly.config; mv temp alignAssembly.config; chmod a+x alignAssembly.config
3 Adjusted alignAssembly.config
3 ln -fs /media/kmkocot/Sclerite/MAKER/Cephalodiscus_hodgsoni_training_set/autoAug/seq/genome_clean.fa genome.fasta
3 Reading MySQL variables from /usr/local/bin/PASA_r20140417/pasa_conf/
1 Dropping MySQL database PASACephalodiscus on host localhost.
2 Executing the Alignment Assembly: perl /usr/local/bin/PASA_r20140417/scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g /media/kmkocot/Sclerite/MAKER/Cephalodiscus_hodgsoni_training_set/autoAug/seq/genome_clean.fa -t transcripts.fasta.clean -T -u transcripts.fasta --ALIGNERS blat 1>Launch_PASA_pipeline.stdout 2>Launch_PASA_pipeline.stderr ...2 A test output...
Finished
2 Running perl /usr/local/bin/PASA_r20140417/scripts/pasa_asmbls_to_training_set.dbi -M "PASACephalodiscus:localhost" -p "estpipe:secure" -g /media/kmkocot/Sclerite/MAKER/Cephalodiscus_hodgsoni_training_set/autoAug/seq/genome_clean.fa --pasa_transcripts_fasta mydb.assemblies.fasta --pasa_transcripts_gff3 mydb.pasa_assemblies.gff3 1>pasa_asmbls_to_training_set.stdout 2>pasa_asmbls_to_training_set.stderr ...failed to execute: perl /usr/local/bin/PASA_r20140417/scripts/pasa_asmbls_to_training_set.dbi -M "PASACephalodiscus:localhost" -p "estpipe:secure" -g /media/kmkocot/Sclerite/MAKER/Cephalodiscus_hodgsoni_training_set/autoAug/seq/genome_clean.fa --pasa_transcripts_fasta mydb.assemblies.fasta --pasa_transcripts_gff3 mydb.pasa_assemblies.gff3 1>pasa_asmbls_to_training_set.stdout 2>pasa_asmbls_to_training_set.stderr
kmkocot@Epimenia:/media/kmkocot/Sclerite/MAKER/Cephalodiscus_hodgsoni_training_set$
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Re: autoAug.pl error

Post by katharina »

by Kevin K on 02.06.2014 - 06:46
Just to follow up on my previous post, I see that there is a big difference between pasa_asmbls_to_training_set.dbi in the current version and an older version from 2010 I grabbed but I'm still getting the same error with the older version of the script.
Thanks,
Kevin
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Re: autoAug.pl error

Post by katharina »

by katharina on 03.06.2014 - 14:36
Are you 100% sure that you don't have the newer pasa version in your $PATH variable? Does autoAug.pl actually use the old pasa version?
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