Re: [galaxy-dev] Failing test in tool shed not shown

11 Jun 2013

      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
<bjoern.gruening@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.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 (mario.stanke@uni-greifswald.de) -# and Oliver Keller (keller@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.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 (mario.stanke@uni-greifswald.de) -# and Oliver Keller (keller@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.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 (mario.stanke@uni-greifswald.de) -# and Oliver Keller (keller@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