On Tue, Jun 11, 2013 at 9:18 AM, Björn Grüning <
bjoern.gruen...@pharmazie.uni-freiburg.de> 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.gtfv.
/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 (mario.sta...@uni-greifswald.de)
-# and Oliver Keller (kel...@cs.uni-goettingen.de). -# 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.gffv.
/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 (
mario.sta...@uni-greifswald.de) -# and Oliver Keller (
kel...@cs.uni-goettingen.de). -# 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.gtfv.
/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 (mario.sta...@uni-greifswald.de)
-# and Oliver Keller (kel...@cs.uni-goettingen.de). -# 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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