Question: usegalaxy build snpEff database via genbank
1
gravatar for atasaral
25 days ago by
atasaral10
atasaral10 wrote:

Hello, I have built the SnpEff4.3 database for Salmo salar's chromosome 25 from Genbank and I have analyzed with SnpEff eff: annotate variants (Galaxy Version 4.3+T.galaxy2).I have obtained results for Chromosome 25. Now, I need to keep at the analyzing for the other chromosomes. For example, I did for Chromosome 8 and 9 exactly the same way but It didn't build SnpEff4.3 databases for them. But I built for chromosome 28 also. I need for all chromosomes. Please help me to solve this problem. I am using usegalaxy The error message as follow:

Fatal error: Exit code 255 (Error) Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/019/880/19880994/_job_tmp -Xmx7g -Xms256m 00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani 00:00:00 Command: 'build' 00:00:00 Building database for 'ssa08' 00:00:00 Reading configuration file 'snpEff.config'. Genome: 'ssa08' 00:00:00 Reading config file: /galaxy-repl/main/jobdir/019/880/19880994/working/snpEff.config 00:00:00 Reading config file: /cvmfs/main.galaxyproject.org/deps/_conda/pkgs/snpeff-4.3.1t-0/share/snpeff-4.3.1t-0/snpEff.config 00:00:01 done Chromosome: 'ssa08' length: 26434011 java.lang.RuntimeException: Transcript 'NM_001140227.1' is already in Gene 'GeneID:100195198' at org.snpeff.interval.IntervalAndSubIntervals.add(IntervalAndSubIntervals.java:44) at org.snpeff.snpEffect.factory.SnpEffPredictorFactory.add(SnpEffPredictorFactory.java:133) at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.addMrna(SnpEffPredictorFactoryFeatures.java:183) at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.addFeatures(SnpEffPredictorFactoryFeatures.java:134) at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:330) at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:369) at org.snpeff.SnpEff.run(SnpEff.java:1183) at org.snpeff.SnpEff.main(SnpEff.java:162) java.lang.RuntimeException: Error reading file '/galaxy-repl/main/jobdir/019/880/19880994/dataset_25853021_files/ssa08/genes.gbk' java.lang.RuntimeException: Transcript 'NM_001140227.1' is already in Gene 'GeneID:100195198' at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:344) at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:369) at org.snpeff.SnpEff.run(SnpEff.java:1183) at org.snpeff.SnpEff.main(SnpEff.java:162) 00:00:08 Logging 00:00:09 Checking for updates... 00:00:10 Done.

galaxy • 107 views
ADD COMMENTlink modified 10 days ago • written 25 days ago by atasaral10
0
gravatar for Anton Nekrutenko
25 days ago by
Penn State
Anton Nekrutenko1.7k wrote:

Have you tried to create the DB from entire Salmon genome: https://www.ncbi.nlm.nih.gov/nuccore/925216783?report=genbank

ADD COMMENTlink written 25 days ago by Anton Nekrutenko1.7k

Yes, Anton I have tried from this website for chromosome 25. And it worked. But When I tried for the other chromosome such as 8 and 9 it didn't. I followed on this link http://snpeff.sourceforge.net/SnpEff_manual.html#databases with this steps Option 4: Building a database from GenBank files When I added to usegalaxy the entire genome files it does not recognize them also. For this reaosn I was trying to build chromosome by chromosome.

ADD REPLYlink modified 25 days ago • written 25 days ago by atasaral10
0
gravatar for Anton Nekrutenko
25 days ago by
Penn State
Anton Nekrutenko1.7k wrote:

This seems like SnpEff issue. If I understand correctly, Salmon genome assembly is highly fragmented and so the same gene can be split between several scaffolds. This is likely what is happening here. Let me take a closer look.

ADD COMMENTlink written 25 days ago by Anton Nekrutenko1.7k

I really appreciate it. Thank you very much. I look forward to your reply.

ADD REPLYlink written 25 days ago by atasaral10
0
gravatar for Anton Nekrutenko
25 days ago by
Penn State
Anton Nekrutenko1.7k wrote:

Yes, it is the result of fragmented genome. We will try to modify SnpEff build to accept GFF in the next few days.

ADD COMMENTlink modified 25 days ago • written 25 days ago by Anton Nekrutenko1.7k

Your support is very significant for my research. I really thankful for it. I am looking forward to hearing from you.

ADD REPLYlink written 25 days ago by atasaral10
0
gravatar for atasaral
10 days ago by
atasaral10
atasaral10 wrote:

Hello Anton, Thank you for modifying it. Sincerely, Sebnem

ADD COMMENTlink written 10 days ago by atasaral10
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