test/base/twilltestcase.py - Converting local (test-data) bam to sam failed
Hi all, I have a query about a failing tool test on the Tool Shed, where it seems Galaxy is trying to convert both the expected BAM output and the tool's BAM output into SAM for comparison - but this fails. https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad 2015-01-27 02:13:51 ... Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1) Stderr: Traceback: Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 122, in test_tool self.do_it( td ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 40, in do_it self._verify_outputs( testdef, test_history, jobs, shed_tool_id, data_list, galaxy_interactor ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 80, in _verify_outputs galaxy_interactor.verify_output( history, jobs, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 66, in verify_output self.twill_test_case.verify_hid( outfile, hda_id=hid, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 2341, in verify_hid raise AssertionError( errmsg ) AssertionError: History item different than expected, difference (using diff): ( /tmp/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/2d303f2e09e0/samtools_depad/test-data/sam_spec_padded.depad.bam v. /tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpExQWRD/tmpSknKqLsam_spec_padded.depad.bam ) Converting local (test-data) bam to sam failed (and same error on the second test) The same occurs on the Test Tool Shed (with a very slightly updated version of this tool), although with a more concise traceback: https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad 2015-01-25 08:21:59 ... Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2) Stderr: Traceback: Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 268, in test_tool self.do_it( td ) File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in do_it raise e JobOutputsError: History item different than expected, difference (using diff): ( /tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/8e1e3a1ecad7/samtools_depad/test-data/sam_spec_padded.depad.bam v. /tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpNvCGJi/tmphX3A_Fsam_spec_padded.depad.bam ) Converting local (test-data) bam to sam failed Both tests should produce a BAM file matching the provided test-data/sam_spec_padded.depad.bam example. The error comes from test/base/twilltestcase.py, p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_local.name, local_name ), shell=True ) assert not p.wait(), 'Converting local (test-data) bam to sam failed' Running this command locally at the terminal seems to work fine, both with samtools 0.1.19 and 1.1. $ ~/bin/samtools_0.1.19 view -h -o temp.sam sam_spec_padded.depad.bam $ more temp.sam @HD VN:1.5 SO:coordinate @SQ SN:ref LN:45 ref 516 ref 1 0 45M * 0 0 AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT * r001 99 ref 7 30 8M2I4M1D3M = 37 41 TTAGATAAAGGATACTG * * 768 ref 8 30 1M * 0 0 * * CT:Z:.;Warning;Note=Ref wrong? r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * PT:Z:1;4;+;homopolymer r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 r004 0 ref 16 30 6M14D5M * 0 0 ATAGCTTCAGC * r003 2064 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 r001 147 ref 37 30 9M = 7 -41 CAGCGGCAT * NM:i:1 $ ~/bin/samtools_1.1 view -h -o temp.sam sam_spec_padded.depad.bam [galaxy@ppserver test-data]$ more temp.sam @HD VN:1.5 SO:coordinate @SQ SN:ref LN:45 ref 516 ref 1 0 45M * 0 0 AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT * r001 99 ref 7 30 8M2I4M1D3M = 37 41 TTAGATAAAGGATACTG * * 768 ref 8 30 1M * 0 0 * * CT:Z:.;Warning;Note=Ref wrong? r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * PT:Z:1;4;+;homopolymer r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 r004 0 ref 16 30 6M14D5M * 0 0 ATAGCTTCAGC * r003 2064 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 r001 147 ref 37 30 9M = 7 -41 CAGCGGCAT * NM:i:1 Which version of samtools is on the $PATH on the test system? Could the test system have run out of disk space again? The tests are passing on my local development instance (before and after updating to latest galaxy-central), and on TravisCI using the latest Galaxy: https://travis-ci.org/peterjc/pico_galaxy/builds/48485673 Thanks, Peter
On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
I have a query about a failing tool test on the Tool Shed, where it seems Galaxy is trying to convert both the expected BAM output and the tool's BAM output into SAM for comparison - but this fails.
https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
2015-01-27 02:13:51 ... Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1) Stderr: Traceback: Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 122, in test_tool self.do_it( td ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 40, in do_it self._verify_outputs( testdef, test_history, jobs, shed_tool_id, data_list, galaxy_interactor ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 80, in _verify_outputs galaxy_interactor.verify_output( history, jobs, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 66, in verify_output self.twill_test_case.verify_hid( outfile, hda_id=hid, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 2341, in verify_hid raise AssertionError( errmsg ) AssertionError: History item different than expected, difference (using diff): ( /tmp/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/2d303f2e09e0/samtools_depad/test-data/sam_spec_padded.depad.bam v. /tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpExQWRD/tmpSknKqLsam_spec_padded.depad.bam ) Converting local (test-data) bam to sam failed
(and same error on the second test)
https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad is still failing, although now with a more concise traceback: Test runs 2015-01-29 02:26:31 Automated test environment Tests that failed Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1) Stderr: Traceback: Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 122, in test_tool self.do_it( td ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 40, in do_it self._verify_outputs( testdef, test_history, jobs, shed_tool_id, data_list, galaxy_interactor ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 80, in _verify_outputs galaxy_interactor.verify_output( history, jobs, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 66, in verify_output self.twill_test_case.verify_hid( outfile, hda_id=hid, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id ) File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 2341, in verify_hid raise AssertionError( errmsg ) AssertionError: History item different than expected, difference (using diff): ( /tmp/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/2d303f2e09e0/samtools_depad/test-data/sam_spec_padded.depad.bam v. /tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpfD5MDC/tmpOpbQxNsam_spec_padded.depad.bam ) Converting local (test-data) bam to sam failed
The same occurs on the Test Tool Shed (with a very slightly updated version of this tool), although with a more concise traceback:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
2015-01-25 08:21:59 ... Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2) Stderr: Traceback: Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 268, in test_tool self.do_it( td ) File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in do_it raise e JobOutputsError: History item different than expected, difference (using diff): ( /tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/8e1e3a1ecad7/samtools_depad/test-data/sam_spec_padded.depad.bam v. /tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpNvCGJi/tmphX3A_Fsam_spec_padded.depad.bam ) Converting local (test-data) bam to sam failed
https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad also still failing, Test runs 2015-01-25 08:21:59 Automated test environment Tests that failed Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2) Stderr: Traceback: Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 268, in test_tool self.do_it( td ) File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in do_it raise e JobOutputsError: History item different than expected, difference (using diff): ( /tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/8e1e3a1ecad7/samtools_depad/test-data/sam_spec_padded.depad.bam v. /tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpNvCGJi/tmphX3A_Fsam_spec_padded.depad.bam ) Converting local (test-data) bam to sam failed
Both tests should produce a BAM file matching the provided test-data/sam_spec_padded.depad.bam example. The error comes from test/base/twilltestcase.py,
p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_local.name, local_name ), shell=True ) assert not p.wait(), 'Converting local (test-data) bam to sam failed'
Running this command locally at the terminal seems to work fine, both with samtools 0.1.19 and 1.1.
$ ~/bin/samtools_0.1.19 view -h -o temp.sam sam_spec_padded.depad.bam $ more temp.sam @HD VN:1.5 SO:coordinate @SQ SN:ref LN:45 ref 516 ref 1 0 45M * 0 0 AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT * r001 99 ref 7 30 8M2I4M1D3M = 37 41 TTAGATAAAGGATACTG * * 768 ref 8 30 1M * 0 0 * * CT:Z:.;Warning;Note=Ref wrong? r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * PT:Z:1;4;+;homopolymer r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 r004 0 ref 16 30 6M14D5M * 0 0 ATAGCTTCAGC * r003 2064 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 r001 147 ref 37 30 9M = 7 -41 CAGCGGCAT * NM:i:1
$ ~/bin/samtools_1.1 view -h -o temp.sam sam_spec_padded.depad.bam [galaxy@ppserver test-data]$ more temp.sam @HD VN:1.5 SO:coordinate @SQ SN:ref LN:45 ref 516 ref 1 0 45M * 0 0 AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT * r001 99 ref 7 30 8M2I4M1D3M = 37 41 TTAGATAAAGGATACTG * * 768 ref 8 30 1M * 0 0 * * CT:Z:.;Warning;Note=Ref wrong? r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * PT:Z:1;4;+;homopolymer r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 r004 0 ref 16 30 6M14D5M * 0 0 ATAGCTTCAGC * r003 2064 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 r001 147 ref 37 30 9M = 7 -41 CAGCGGCAT * NM:i:1
Which version of samtools is on the $PATH on the test system?
Could the test system have run out of disk space again?
The tests are passing on my local development instance (before and after updating to latest galaxy-central), and on TravisCI using the latest Galaxy: https://travis-ci.org/peterjc/pico_galaxy/builds/48485673
Thanks,
Peter
Any ideas? Are any of the other tools on either Tool Shed showing the same error? Thanks, Peter
On Tue, Mar 3, 2015 at 9:55 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
I have a query about a failing tool test on the Tool Shed, where it seems Galaxy is trying to convert both the expected BAM output and the tool's BAM output into SAM for comparison - but this fails.
https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
2015-01-27 02:13:51 ... Converting local (test-data) bam to sam failed
(and same error on the second test)
https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad is still failing, although now with a more concise traceback:
Test runs 2015-01-29 02:26:31 Automated test environment Tests that failed Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1) Stderr: Traceback: Traceback (most recent call last): ... Converting local (test-data) bam to sam failed
The same occurs on the Test Tool Shed (with a very slightly updated version of this tool), although with a more concise traceback:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
2015-01-25 08:21:59 ... Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2) Stderr: Traceback: ... Converting local (test-data) bam to sam failed
https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad also still failing,
Test runs 2015-01-25 08:21:59 ... Converting local (test-data) bam to sam failed
Still failing on the Test Tool Shed, bug filed on Trello, https://trello.com/c/TL0IdLlG/2570-toolshed-converting-local-test-data-bam-t... Tests currently stalled on the main Tool Shed, reported here: http://dev.list.galaxyproject.org/Tests-not-being-run-on-toolsheds-tc4666816... https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-March/021708.html Peter
Hey Peter, Thanks for continuing to apply pressure on these issues. I have pushed some logging into Galaxy's development branch (https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e...) that should make that error more informative. I don't know when that will get pushed out to bitbucket and the shed retested - but once those two things happen we will hopefully have a better idea what the problem is (probably some subtle deployment problem - some incompatible version of samtools on the path? samtools on Galaxy's path but not the test script's path?). -John On Mon, Mar 23, 2015 at 6:06 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Mar 3, 2015 at 9:55 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
I have a query about a failing tool test on the Tool Shed, where it seems Galaxy is trying to convert both the expected BAM output and the tool's BAM output into SAM for comparison - but this fails.
https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
2015-01-27 02:13:51 ... Converting local (test-data) bam to sam failed
(and same error on the second test)
https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad is still failing, although now with a more concise traceback:
Test runs 2015-01-29 02:26:31 Automated test environment Tests that failed Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1) Stderr: Traceback: Traceback (most recent call last): ... Converting local (test-data) bam to sam failed
The same occurs on the Test Tool Shed (with a very slightly updated version of this tool), although with a more concise traceback:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
2015-01-25 08:21:59 ... Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2) Stderr: Traceback: ... Converting local (test-data) bam to sam failed
https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad also still failing,
Test runs 2015-01-25 08:21:59 ... Converting local (test-data) bam to sam failed
Still failing on the Test Tool Shed, bug filed on Trello, https://trello.com/c/TL0IdLlG/2570-toolshed-converting-local-test-data-bam-t...
Tests currently stalled on the main Tool Shed, reported here: http://dev.list.galaxyproject.org/Tests-not-being-run-on-toolsheds-tc4666816... https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-March/021708.html
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On Mon, Mar 23, 2015 at 1:41 PM, John Chilton <jmchilton@gmail.com> wrote:
Hey Peter,
Thanks for continuing to apply pressure on these issues. I have pushed some logging into Galaxy's development branch (https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e...) that should make that error more informative. I don't know when that will get pushed out to bitbucket and the shed retested - but once those two things happen we will hopefully have a better idea what the problem is (probably some subtle deployment problem - some incompatible version of samtools on the path? samtools on Galaxy's path but not the test script's path?).
-John
Lovely - I agree this seems the most likely cause, so fingers crossed. Thank you, Peter
On Mon, Mar 23, 2015 at 4:00 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Mar 23, 2015 at 1:41 PM, John Chilton <jmchilton@gmail.com> wrote:
Hey Peter,
Thanks for continuing to apply pressure on these issues. I have pushed some logging into Galaxy's development branch (https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e...) that should make that error more informative. I don't know when that will get pushed out to bitbucket and the shed retested - but once those two things happen we will hopefully have a better idea what the problem is (probably some subtle deployment problem - some incompatible version of samtools on the path? samtools on Galaxy's path but not the test script's path?).
-John
Lovely - I agree this seems the most likely cause, so fingers crossed.
Thank you,
Peter
Sadly this tool hasn't been tested since 2015-03-18 so we don't yet know what extra clues your debug logging will reveal... https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad/ Peter
participants (2)
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John Chilton -
Peter Cock