I get an error during annotation, when the process bar stops at 85%, that looks like this on the terminal:
Metawatt [INFO|6:49:52] Initializing annotations ...
Metawatt [INFO|6:49:52] Blast database taxonomic rank: genus
Metawatt [INFO|6:49:52] Minimum aligned length (blast): 200
Metawatt [INFO|6:49:52] Minimum percent ID (blast): 25 %
Metawatt [INFO|6:49:52] Computing coverage and percent GC ...
Metawatt [INFO|6:49:52] Percent GC calculation and coverage parsing errors: 0
Metawatt [INFO|6:49:52] Fragmenting contigs (file /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments) ...
Metawatt [INFO|6:49:52] Fragmenting; fragment length 500, step 1, fragments (estimated) 29740, files 20
Metawatt [INFO|6:49:52] Actual fragments in file 0: 1634
Metawatt [INFO|6:49:52] Actual fragments in file 1: 1495
…. and so on ....
Metawatt [INFO|6:49:53] Actual fragments in file 18: 1490
Metawatt [INFO|6:49:53] Actual fragments in file 19: 1057
Metawatt [INFO|6:49:53] Total fragments in all files: 29740
Metawatt [INFO|6:49:53] Fragment length: 500
Metawatt [INFO|6:49:53] Fragments created: 29740
Metawatt [INFO|6:49:53] /home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27/bin/blastn -num_descriptions 10 -num_alignments 10 -outfmt 6 -evalue 1e-3 -max_target_seqs 10 -db /home/ana/Escritorio/CNB/Metawatt/blastdb -query /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments.0.fragments -out /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments.0.fragments.blast
…. and so on ....
Metawatt [INFO|6:50:12] /home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27/bin/blastn -num_descriptions 10 -num_alignments 10 -outfmt 6 -evalue 1e-3 -max_target_seqs 10 -db /home/ana/Escritorio/CNB/Metawatt/blastdb -query /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments.19.fragments -out /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments.19.fragments.blast
Metawatt [INFO|6:50:14] incomplete - ended with error
I could actually see the files at the temp directory, but suddenly they disappeared after quitting Metawatt (only an empty MSO_GATC.fna.fragments.blast is saved), even when I saved the project...
At the terminal reads:
Metawatt [SEVERE|6:50:14] Script returned error
java.io.FileNotFoundException: /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments.0.fragments.blast (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:137)
at java.io.FileReader.<init>(FileReader.java:72)
at org.metawatt.external.BlastFactory.runBlast(BlastFactory.java:211)
at org.metawatt.scripts.ContigAnnotator.runScript(ContigAnnotator.java:207)
at org.metawatt.scripts.AbstractScript.doInBackground(AbstractScript.java:62)
at org.metawatt.scripts.AbstractScript.doInBackground(AbstractScript.java:22)
at javax.swing.SwingWorker$1.call(SwingWorker.java:291)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at javax.swing.SwingWorker.run(SwingWorker.java:330)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:679)</init></init>
Finally, the dependency problems were solved (blast, glimmer and baltik are OK) and I had successfully generated the blastdb from the taxonomyfile that you provided (after deleting several genomes that keep giving errors).
What could I try?
Best,
Ana
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Hi Ana
Did you ever find a solution for the problem that the annotation did not work and that you got an error message (file not found) when the status bar was at 85%?
I ran into the same problem and have so far not been able to solve it.
I would be grateful for any suggestions that you might have.
Manuel
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Based on your output, I think the blast program was never started. On
some unix/linux systems java has no access to the systems $PATH. I think
Ana fixed this by specifying the path when you call metawatt on the
command line:
Take care: you need to specify the path of the folder that contains the
blastn and makeblastdb executables. Also make sure that it really
created the blastdb before you click "annotate".
Can you check if this works?
Best wishes,
Marc
On 03/25/13 03:51, Manuel Kleiner wrote:
Hi Ana
Did you ever find a solution for the problem that the annotation did not work and that you got an error message (file not found) when the status bar was at 85%?
I ran into the same problem and have so far not been able to solve it.
I would be grateful for any suggestions that you might have.
Manuel
--
Prof. dr. ir. Marc Strous
Head of the Microbial Fitness Group
Max Planck Institute for Marine Microbiology
Celciusstrasse 1 - 28359 Bremen - Germany
phone 0421 2028 822 | fax 0421 2028 580
room 3241
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Also, when I try to open the test.metawattproject, it is not loading.. then in terminal I get the same script returned error from java. In this case the taxonomyfile from the test is not found.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Marc,
I get an error during annotation, when the process bar stops at 85%, that looks like this on the terminal:
Metawatt [INFO|6:49:52] Initializing annotations ...
Metawatt [INFO|6:49:52] Blast database taxonomic rank: genus
Metawatt [INFO|6:49:52] Minimum aligned length (blast): 200
Metawatt [INFO|6:49:52] Minimum percent ID (blast): 25 %
Metawatt [INFO|6:49:52] Computing coverage and percent GC ...
Metawatt [INFO|6:49:52] Percent GC calculation and coverage parsing errors: 0
Metawatt [INFO|6:49:52] Fragmenting contigs (file /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments) ...
Metawatt [INFO|6:49:52] Fragmenting; fragment length 500, step 1, fragments (estimated) 29740, files 20
Metawatt [INFO|6:49:52] Actual fragments in file 0: 1634
Metawatt [INFO|6:49:52] Actual fragments in file 1: 1495
…. and so on ....
Metawatt [INFO|6:49:53] Actual fragments in file 18: 1490
Metawatt [INFO|6:49:53] Actual fragments in file 19: 1057
Metawatt [INFO|6:49:53] Total fragments in all files: 29740
Metawatt [INFO|6:49:53] Fragment length: 500
Metawatt [INFO|6:49:53] Fragments created: 29740
Metawatt [INFO|6:49:53] /home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27/bin/blastn -num_descriptions 10 -num_alignments 10 -outfmt 6 -evalue 1e-3 -max_target_seqs 10 -db /home/ana/Escritorio/CNB/Metawatt/blastdb -query /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments.0.fragments -out /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments.0.fragments.blast
…. and so on ....
Metawatt [INFO|6:50:12] /home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27/bin/blastn -num_descriptions 10 -num_alignments 10 -outfmt 6 -evalue 1e-3 -max_target_seqs 10 -db /home/ana/Escritorio/CNB/Metawatt/blastdb -query /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments.19.fragments -out /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments.19.fragments.blast
Metawatt [INFO|6:50:14] incomplete - ended with error
I could actually see the files at the temp directory, but suddenly they disappeared after quitting Metawatt (only an empty MSO_GATC.fna.fragments.blast is saved), even when I saved the project...
At the terminal reads:
Metawatt [SEVERE|6:50:14] Script returned error
java.io.FileNotFoundException: /home/ana/Escritorio/CNB/Metawatt/temp/MSO_GATC.fna.fragments.0.fragments.blast (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:137)
at java.io.FileReader.<init>(FileReader.java:72)
at org.metawatt.external.BlastFactory.runBlast(BlastFactory.java:211)
at org.metawatt.scripts.ContigAnnotator.runScript(ContigAnnotator.java:207)
at org.metawatt.scripts.AbstractScript.doInBackground(AbstractScript.java:62)
at org.metawatt.scripts.AbstractScript.doInBackground(AbstractScript.java:22)
at javax.swing.SwingWorker$1.call(SwingWorker.java:291)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at javax.swing.SwingWorker.run(SwingWorker.java:330)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:679)</init></init>
Finally, the dependency problems were solved (blast, glimmer and baltik are OK) and I had successfully generated the blastdb from the taxonomyfile that you provided (after deleting several genomes that keep giving errors).
What could I try?
Best,
Ana
Hi Ana
Did you ever find a solution for the problem that the annotation did not work and that you got an error message (file not found) when the status bar was at 85%?
I ran into the same problem and have so far not been able to solve it.
I would be grateful for any suggestions that you might have.
Manuel
Hi Manuel,
Based on your output, I think the blast program was never started. On
some unix/linux systems java has no access to the systems $PATH. I think
Ana fixed this by specifying the path when you call metawatt on the
command line:
java -jar metawatt.jar -blast=/path/to/blast/execs
as described in the wiki.
Take care: you need to specify the path of the folder that contains the
blastn and makeblastdb executables. Also make sure that it really
created the blastdb before you click "annotate".
Can you check if this works?
Best wishes,
Marc
On 03/25/13 03:51, Manuel Kleiner wrote:
--
Prof. dr. ir. Marc Strous
Head of the Microbial Fitness Group
Max Planck Institute for Marine Microbiology
Celciusstrasse 1 - 28359 Bremen - Germany
phone 0421 2028 822 | fax 0421 2028 580
room 3241
Great, thank you Marc. That fixed the problem.
all the best
Manuel
Also, when I try to open the test.metawattproject, it is not loading.. then in terminal I get the same script returned error from java. In this case the taxonomyfile from the test is not found.