Failing test in tool shed not shown

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Failing test in tool shed not shown

Björn Grüning
Hi,

my augustus repository is shown under the summary page "Latest revision:
failing tool tests" but I could not see any failing test in the
repository.

http://testtoolshed.g2.bx.psu.edu/view/bgruening/augustus

Cheers,
Björn

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Re: Failing test in tool shed not shown

Peter Cock
On Tue, Jun 11, 2013 at 9:18 AM, Björn Grüning <[hidden email]> wrote:
> Hi,
>
> my augustus repository is shown under the summary page "Latest revision:
> failing tool tests" but I could not see any failing test in the
> repository.
>
> http://testtoolshed.g2.bx.psu.edu/view/bgruening/augustus
>
> Cheers,
> Björn

This sounds like the problem I've been having with missing test results.

What is interesting is I can see the augustus failure, which does seem
to support this being at least partly a caching problem. Test failure
below for your reference.

Regards,

Peter

--

Time tested: ~ 10 hours ago
System: Linux 3.5.0-21-generic
Architecture: x86_64
Python version: 2.7.3
Galaxy revision: 9982:8d96629131b0
Galaxy database version: 115
Tool shed revision: 9981:88873eed0092
Tool shed database version: 19
Tool shed mercurial version: 2.2.3
Tool id: augustus
Tool version: augustus
Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
Stderr:
Traceback:
Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/human_augustus_utr-on.gtf v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmpsxWN7Ahuman_augustus_utr-on.gtf ) --- local_file +++ history_data @@ -1,80 +1,35 @@ -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke ([hidden email]) -# and Oliver Keller ([hidden email]). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# Initialising the parameters ... -# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl -# Looks like ./examples/example.fa is in fasta format. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- -# -# Constraints/Hints: -# (none) -# Predicted genes for sequence number 1 on both strands -# start gene g1 -HS04636 AUGUSTUS gene 836 8857 1 + . g1 -HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 -HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1";
Tool id: augustus
Tool version: augustus
Test: test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
Stderr:
Traceback:
Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/human_augustus_utr-on.gff v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmp_tbQfYhuman_augustus_utr-on.gff ) --- local_file +++ history_data @@ -1,77 +1,35 @@ -##gff-version 3 -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke ([hidden email]) -# and Oliver Keller ([hidden email]). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# Initialising the parameters ... -# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl -# Looks like ./examples/example.fa is in fasta format. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- -# -# Predicted genes for sequence number 1 on both strands -# start gene g1 -HS04636 AUGUSTUS gene 836 8857 1 + . ID=g1 -HS04636 AUGUSTUS transcript 836 8857 . + . ID=g1.t1;Parent=g1 -HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=g1.t1 -HS04636 AUGUSTUS exon 836 1017 . + . Parent=g1.t1 -HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=g1.t1 -HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 1818 1934 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 2055 2198 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 2852 2995 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 3426 3607 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 4340 4423 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 4543 4789 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 5072 5358 . + . Parent=g1.t1
Tool id: augustus
Tool version: augustus
Test: test_tool_000002 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
Stderr:
Traceback:
Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmp7_kw_5arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf ) --- local_file +++ history_data @@ -1,85 +1,35 @@ -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke ([hidden email]) -# and Oliver Keller ([hidden email]). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# arabidopsis version. Using default transition matrix. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# ----- prediction on sequence number 1 (length = 2066, name = arabidopsis) ----- -# -# Constraints/Hints: -# (none) -# Predicted genes for sequence number 1 on both strands -# start gene g1 -arabidopsis AUGUSTUS gene 775 1851 0 + . g1 -arabidopsis AUGUSTUS transcript 775 1851 . + . g1.t1 -arabidopsis AUGUSTUS start_codon 775 777 . + 0 transcript_id "g1.t1"; gene_id "g1"; -arabidopsis AUGUSTUS CDS 775 1851 0.99 + 0 transcript_id "g1.t1"; gene_id "g1"; -arabidopsis AUGUSTUS stop_codon 1849 1851 . + 0 transcript_id "g1.t1"; gene_id "g1"; -# protein sequence = [MDLSLAPTTTTSSDQEQDRDQELTSNIGASSSSGPSGNNNNLPMMMIPPPEKEHMFDKVVTPSDVGKLNRLVIPKQHA -# ERYFPLDSSNNQNGTLLNFQDRNGKMWRFRYSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGIGDESERSKLYIDWRHRPDMSLVQAHQFGNFG -# FNFNFPTTSQYSNRFHPLPEYNSVPIHRGLNIGNHQRSYYNTQRQEFVGYGYGNLAGRCYYTGSPLDHRNIVGSEPLVIDSVPVVPGRLTPVMLPPLP -# PPPSTAGKRLRLFGVNMECGNDYNQQEESWLVPRGEIGASSSSSSALRLNLSTDHDDDNDDGDDGDDDQFAKKGKSSLSLNFNP] -# end gene g1 -### -# start gene g2 -arabidopsis AUGUSTUS gene 841 1661 . - . g2 -arabidopsis AUGUSTUS transcript 841 1661 . - . g2.t1 -arabidopsis AUGUSTUS stop_codon 841 843 . - 0 transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS intron 1024 1101 0.75 - . transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS intron 1193 1325 0.03 - . transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS intron 1416 1512 0.85 - . transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS CDS 841 1023 0.87 - 0 transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS CDS 1102 1192 0.78 - 1 transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS CDS 1326 1415 0.05 - 1 transcript_id "g2.t1"; gene_id "g2";
Tool id: augustus
Tool version: augustus
Test: test_tool_000003 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
Stderr:
Traceback:
Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 97, in do_it elem = data_list[ elem_index ] IndexError: list index out of range



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Re: Failing test in tool shed not shown

Björn Grüning
Hi Peter,

Indeed a caching issue.

Any chance we can improve that output? The diff is not really helpful.

Thannks,
Björn

> On Tue, Jun 11, 2013 at 9:18 AM, Björn Grüning
> <[hidden email]> wrote:
> > Hi,
> >
> > my augustus repository is shown under the summary page "Latest
> revision:
> > failing tool tests" but I could not see any failing test in the
> > repository.
> >
> > http://testtoolshed.g2.bx.psu.edu/view/bgruening/augustus
> >
> > Cheers,
> > Björn
>
> This sounds like the problem I've been having with missing test
> results.
>
> What is interesting is I can see the augustus failure, which does seem
> to support this being at least partly a caching problem. Test failure
> below for your reference.
>
> Regards,
>
> Peter
>
> --
>
> Tool test results
> Automated test environment
> Time tested: ~ 10 hours ago
> System: Linux 3.5.0-21-generic
> Architecture: x86_64
> Python version: 2.7.3
> Galaxy revision: 9982:8d96629131b0
> Galaxy database version: 115
> Tool shed revision: 9981:88873eed0092
> Tool shed database version: 19
> Tool shed mercurial version: 2.2.3
> Tests that failed
> Tool id: augustus
> Tool version: augustus
> Test: test_tool_000000
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
> Stderr:
>
> Traceback:
> Traceback (most recent call last): File
> "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/human_augustus_utr-on.gtf v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmpsxWN7Ahuman_augustus_utr-on.gtf ) --- local_file +++ history_data @@ -1,80 +1,35 @@ -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke ([hidden email]) -# and Oliver Keller ([hidden email]). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# Initialising the parameters ... -# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl -# Looks like ./examples/example.fa is in fasta format. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- -# -# Constraints/Hints: -# (none) -# Predicted genes for sequence number 1 on both strands -# start gene g1 -HS04636 AUGUSTUS gene 836 8857 1 + . g1 -HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 -HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1";
> Tool id: augustus
> Tool version: augustus
> Test: test_tool_000001
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
> Stderr:
>
> Traceback:
> Traceback (most recent call last): File
> "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/human_augustus_utr-on.gff v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmp_tbQfYhuman_augustus_utr-on.gff ) --- local_file +++ history_data @@ -1,77 +1,35 @@ -##gff-version 3 -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke ([hidden email]) -# and Oliver Keller ([hidden email]). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# Initialising the parameters ... -# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl -# Looks like ./examples/example.fa is in fasta format. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- -# -# Predicted genes for sequence number 1 on both strands -# start gene g1 -HS04636 AUGUSTUS gene 836 8857 1 + . ID=g1 -HS04636 AUGUSTUS transcript 836 8857 . + . ID=g1.t1;Parent=g1 -HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=g1.t1 -HS04636 AUGUSTUS exon 836 1017 . + . Parent=g1.t1 -HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=g1.t1 -HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 1818 1934 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 2055 2198 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 2852 2995 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 3426 3607 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 4340 4423 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 4543 4789 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 5072 5358 . + . Parent=g1.t1
> Tool id: augustus
> Tool version: augustus
> Test: test_tool_000002
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
> Stderr:
>
> Traceback:
> Traceback (most recent call last): File
> "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmp7_kw_5arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf ) --- local_file +++ history_data @@ -1,85 +1,35 @@ -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke ([hidden email]) -# and Oliver Keller ([hidden email]). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# arabidopsis version. Using default transition matrix. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# ----- prediction on sequence number 1 (length = 2066, name = arabidopsis) ----- -# -# Constraints/Hints: -# (none) -# Predicted genes for sequence number 1 on both strands -# start gene g1 -arabidopsis AUGUSTUS gene 775 1851 0 + . g1 -arabidopsis AUGUSTUS transcript 775 1851 . + . g1.t1 -arabidopsis AUGUSTUS start_codon 775 777 . + 0 transcript_id "g1.t1"; gene_id "g1"; -arabidopsis AUGUSTUS CDS 775 1851 0.99 + 0 transcript_id "g1.t1"; gene_id "g1"; -arabidopsis AUGUSTUS stop_codon 1849 1851 . + 0 transcript_id "g1.t1"; gene_id "g1"; -# protein sequence = [MDLSLAPTTTTSSDQEQDRDQELTSNIGASSSSGPSGNNNNLPMMMIPPPEKEHMFDKVVTPSDVGKLNRLVIPKQHA -# ERYFPLDSSNNQNGTLLNFQDRNGKMWRFRYSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGIGDESERSKLYIDWRHRPDMSLVQAHQFGNFG -# FNFNFPTTSQYSNRFHPLPEYNSVPIHRGLNIGNHQRSYYNTQRQEFVGYGYGNLAGRCYYTGSPLDHRNIVGSEPLVIDSVPVVPGRLTPVMLPPLP -# PPPSTAGKRLRLFGVNMECGNDYNQQEESWLVPRGEIGASSSSSSALRLNLSTDHDDDNDDGDDGDDDQFAKKGKSSLSLNFNP] -# end gene g1 -### -# start gene g2 -arabidopsis AUGUSTUS gene 841 1661 . - . g2 -arabidopsis AUGUSTUS transcript 841 1661 . - . g2.t1 -arabidopsis AUGUSTUS stop_codon 841 843 . - 0 transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS intron 1024 1101 0.75 - . transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS intron 1193 1325 0.03 - . transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS intron 1416 1512 0.85 - . transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS CDS 841 1023 0.87 - 0 transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS CDS 1102 1192 0.78 - 1 transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS CDS 1326 1415 0.05 - 1 transcript_id "g2.t1"; gene_id "g2";
> Tool id: augustus
> Tool version: augustus
> Test: test_tool_000003
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
> Stderr:
>
> Traceback:
> Traceback (most recent call last): File
> "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 97, in do_it elem = data_list[ elem_index ] IndexError: list index out of range
>
>




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Re: Failing test in tool shed not shown

Björn Grüning
In reply to this post by Peter Cock
Hi,

is every test shown, also if it runs successfully?
I'm just wondering because there is no installation test shown. And the
diff (is it truncated after X lines?) looks like the entire output is
missing.

Ciao,
Björn


> On Tue, Jun 11, 2013 at 9:18 AM, Björn Grüning
> <[hidden email]> wrote:
> > Hi,
> >
> > my augustus repository is shown under the summary page "Latest
> revision:
> > failing tool tests" but I could not see any failing test in the
> > repository.
> >
> > http://testtoolshed.g2.bx.psu.edu/view/bgruening/augustus
> >
> > Cheers,
> > Björn
>
> This sounds like the problem I've been having with missing test
> results.
>
> What is interesting is I can see the augustus failure, which does seem
> to support this being at least partly a caching problem. Test failure
> below for your reference.
>
> Regards,
>
> Peter
>
> --
>
> Tool test results
> Automated test environment
> Time tested: ~ 10 hours ago
> System: Linux 3.5.0-21-generic
> Architecture: x86_64
> Python version: 2.7.3
> Galaxy revision: 9982:8d96629131b0
> Galaxy database version: 115
> Tool shed revision: 9981:88873eed0092
> Tool shed database version: 19
> Tool shed mercurial version: 2.2.3
> Tests that failed
> Tool id: augustus
> Tool version: augustus
> Test: test_tool_000000
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
> Stderr:
>
> Traceback:
> Traceback (most recent call last): File
> "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/human_augustus_utr-on.gtf v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmpsxWN7Ahuman_augustus_utr-on.gtf ) --- local_file +++ history_data @@ -1,80 +1,35 @@ -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke ([hidden email]) -# and Oliver Keller ([hidden email]). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# Initialising the parameters ... -# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl -# Looks like ./examples/example.fa is in fasta format. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- -# -# Constraints/Hints: -# (none) -# Predicted genes for sequence number 1 on both strands -# start gene g1 -HS04636 AUGUSTUS gene 836 8857 1 + . g1 -HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 -HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1";
> Tool id: augustus
> Tool version: augustus
> Test: test_tool_000001
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
> Stderr:
>
> Traceback:
> Traceback (most recent call last): File
> "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/human_augustus_utr-on.gff v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmp_tbQfYhuman_augustus_utr-on.gff ) --- local_file +++ history_data @@ -1,77 +1,35 @@ -##gff-version 3 -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke ([hidden email]) -# and Oliver Keller ([hidden email]). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# Initialising the parameters ... -# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl -# Looks like ./examples/example.fa is in fasta format. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- -# -# Predicted genes for sequence number 1 on both strands -# start gene g1 -HS04636 AUGUSTUS gene 836 8857 1 + . ID=g1 -HS04636 AUGUSTUS transcript 836 8857 . + . ID=g1.t1;Parent=g1 -HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=g1.t1 -HS04636 AUGUSTUS exon 836 1017 . + . Parent=g1.t1 -HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=g1.t1 -HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 1818 1934 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 2055 2198 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 2852 2995 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 3426 3607 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 4340 4423 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 4543 4789 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 5072 5358 . + . Parent=g1.t1
> Tool id: augustus
> Tool version: augustus
> Test: test_tool_000002
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
> Stderr:
>
> Traceback:
> Traceback (most recent call last): File
> "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmp7_kw_5arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf ) --- local_file +++ history_data @@ -1,85 +1,35 @@ -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke ([hidden email]) -# and Oliver Keller ([hidden email]). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# arabidopsis version. Using default transition matrix. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# ----- prediction on sequence number 1 (length = 2066, name = arabidopsis) ----- -# -# Constraints/Hints: -# (none) -# Predicted genes for sequence number 1 on both strands -# start gene g1 -arabidopsis AUGUSTUS gene 775 1851 0 + . g1 -arabidopsis AUGUSTUS transcript 775 1851 . + . g1.t1 -arabidopsis AUGUSTUS start_codon 775 777 . + 0 transcript_id "g1.t1"; gene_id "g1"; -arabidopsis AUGUSTUS CDS 775 1851 0.99 + 0 transcript_id "g1.t1"; gene_id "g1"; -arabidopsis AUGUSTUS stop_codon 1849 1851 . + 0 transcript_id "g1.t1"; gene_id "g1"; -# protein sequence = [MDLSLAPTTTTSSDQEQDRDQELTSNIGASSSSGPSGNNNNLPMMMIPPPEKEHMFDKVVTPSDVGKLNRLVIPKQHA -# ERYFPLDSSNNQNGTLLNFQDRNGKMWRFRYSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGIGDESERSKLYIDWRHRPDMSLVQAHQFGNFG -# FNFNFPTTSQYSNRFHPLPEYNSVPIHRGLNIGNHQRSYYNTQRQEFVGYGYGNLAGRCYYTGSPLDHRNIVGSEPLVIDSVPVVPGRLTPVMLPPLP -# PPPSTAGKRLRLFGVNMECGNDYNQQEESWLVPRGEIGASSSSSSALRLNLSTDHDDDNDDGDDGDDDQFAKKGKSSLSLNFNP] -# end gene g1 -### -# start gene g2 -arabidopsis AUGUSTUS gene 841 1661 . - . g2 -arabidopsis AUGUSTUS transcript 841 1661 . - . g2.t1 -arabidopsis AUGUSTUS stop_codon 841 843 . - 0 transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS intron 1024 1101 0.75 - . transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS intron 1193 1325 0.03 - . transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS intron 1416 1512 0.85 - . transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS CDS 841 1023 0.87 - 0 transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS CDS 1102 1192 0.78 - 1 transcript_id "g2.t1"; gene_id "g2"; -arabidopsis AUGUSTUS CDS 1326 1415 0.05 - 1 transcript_id "g2.t1"; gene_id "g2";
> Tool id: augustus
> Tool version: augustus
> Test: test_tool_000003
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3)
> Stderr:
>
> Traceback:
> Traceback (most recent call last): File
> "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 97, in do_it elem = data_list[ elem_index ] IndexError: list index out of range
>
>




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