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From: metabase:user:e667a2a9-6c14-1014-9503-c31448f0d22a
Subject: FAIL Bio-VertRes-Config-1.133090 v5.20.0
Date: 2015-01-12T01:40:13Z
This distribution has been tested as part of the CPAN Testers
project, supporting the Perl programming language. See
http://wiki.cpantesters.org/ for more information or email
questions to cpan-testers-discuss@perl.org
--
Dear Andrew Page,
This is a computer-generated report for Bio-VertRes-Config-1.133090
on perl 5.20.0, created by CPAN-Reporter-1.2012.
Thank you for uploading your work to CPAN. However, there was a problem
testing your distribution.
If you think this report is invalid, please consult the CPAN Testers Wiki
for suggestions on how to avoid getting FAIL reports for missing library
or binary dependencies, unsupported operating systems, and so on:
http://wiki.cpantesters.org/wiki/CPANAuthorNotes
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
PROGRAM OUTPUT
------------------------------
Output from 'C:\STRAWB~1\c\bin\dmake.exe test':
C:\Strawberry\perl\bin\perl.exe "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib\lib', 'blib\arch')" t/Bio/VertRes/Config/*.t t/Bio/VertRes/Config/CommandLine/*.t t/Bio/VertRes/Config/Pipelines/*.t t/Bio/VertRes/Config/Recipes/*.t t/bin/*.t
# Failed test 'files created as expected for -d some_other_db_name -t study -i ZZZ -c C:\Users\albie\AppData\Local\Temp\NqbjTEZ3GM -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -c C:\Users\albie\AppData\Local\Temp\Qw2zrenERj -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -c C:\Users\albie\AppData\Local\Temp\1YRdlgnmvl -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -c C:\Users\albie\AppData\Local\Temp\ndQ14zrLqU -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -c C:\Users\albie\AppData\Local\Temp\4G9iEc3FPl -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -c C:\Users\albie\AppData\Local\Temp\XoNkOaAHvW -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\EHXqNyF0ey -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -assembler spades -c C:\Users\albie\AppData\Local\Temp\kOUNX3MkiF -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 8 tests of 8.
t/bin/bacteria_assembly_and_annotation.t ...........................
Dubious, test returned 8 (wstat 2048, 0x800)
Failed 8/8 subtests
# Failed test 'files created as expected for -d some_other_db_name -t study -i ZZZ -c C:\Users\albie\AppData\Local\Temp\bwdqdSnkCq -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -c C:\Users\albie\AppData\Local\Temp\v8H3NQK8CB -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -c C:\Users\albie\AppData\Local\Temp\4TtLWs8m65 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -c C:\Users\albie\AppData\Local\Temp\i80gmHxSLY -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -c C:\Users\albie\AppData\Local\Temp\_B0RgzBwmC -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -c C:\Users\albie\AppData\Local\Temp\fkMcswgW6Y -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 6 tests of 6.
t/bin/bacteria_assembly_single_cell.t ..............................
Dubious, test returned 6 (wstat 1536, 0x600)
Failed 6/6 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\bdGPLhl6jb -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\32LpTFXpwR -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\7HYF5TKDiO -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\Y13686aBMg -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\mB2aObbVrS -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\DGcpopKhuf -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\8mWNtoLPnV -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bwa -c C:\Users\albie\AppData\Local\Temp\vr9x4Wqg3J -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m ssaha2 -c C:\Users\albie\AppData\Local\Temp\lcpavuNJvK -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\zlzONG9PUN -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m tophat -c C:\Users\albie\AppData\Local\Temp\3gNvAPKLlO -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -p StandardProtocol -c C:\Users\albie\AppData\Local\Temp\p7KESZB4Uw -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s "Staphylococcus_aureus" -c C:\Users\albie\AppData\Local\Temp\BcXe2MYsKk -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 13 tests of 13.
t/bin/bacteria_mapping.t ...........................................
Dubious, test returned 13 (wstat 3328, 0xd00)
Failed 13/13 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\BOYBGMc4fp -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -d some_other_db_name -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\C2seINR2_X -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\noRHAHlE3Z -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\Q2yJ_Sa1Pm -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\yGkJfqPK5v -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\_gFQlsoxuO -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\vVyBWssFMA -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -assembler spades -c C:\Users\albie\AppData\Local\Temp\TqMeUZ4ajX -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\UdDBFzww7j -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 9 tests of 9.
t/bin/bacteria_register_and_qc_study.t .............................
Dubious, test returned 9 (wstat 2304, 0x900)
Failed 9/9 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\uTfDUXSNyD -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\_LXTc_HNdX -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\YUiDHN_btt -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\0ZDiZqUwFM -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\D0xpWGwoBb -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\fqrzMkWGRU -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\kxze5FLZwL -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m smalt -c C:\Users\albie\AppData\Local\Temp\VzZdzTdWtz -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\uuxjS2p6AT -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m tophat -c C:\Users\albie\AppData\Local\Temp\fSd3YAMQHt -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -p "StandardProtocol" -c C:\Users\albie\AppData\Local\Temp\wJBjBBHq8I -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\m3lBeNWWQg -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 12 tests of 12.
t/bin/bacteria_rna_seq_expression.t ................................
Dubious, test returned 12 (wstat 3072, 0xc00)
Failed 12/12 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\QTj5kCbn3V -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\Ls3_zyvKDT -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\8Cpw_eJHFn -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\WepFdZbCjG -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\2ZRTI9m6l0 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\v1Pq0qc48n -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\7RJUf7UOBj -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bwa -c C:\Users\albie\AppData\Local\Temp\UcsIx3X1Os -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m ssaha2 -c C:\Users\albie\AppData\Local\Temp\OlvVaFhKYd -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\yttdtYQURW -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\dUscmYilUg -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 11 tests of 11.
t/bin/bacteria_snp_calling.t .......................................
Dubious, test returned 11 (wstat 2816, 0xb00)
Failed 11/11 subtests
# Failed test 'files created as expected for -d some_other_db_name -t study -i ZZZ -c C:\Users\albie\AppData\Local\Temp\0f2MV1R848 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -c C:\Users\albie\AppData\Local\Temp\bbQY70w2fi -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -c C:\Users\albie\AppData\Local\Temp\LPDlUIBrBf -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -c C:\Users\albie\AppData\Local\Temp\YrBjO5ggdQ -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -c C:\Users\albie\AppData\Local\Temp\TspVD0U6mc -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -c C:\Users\albie\AppData\Local\Temp\a7LZoy8DbA -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\AtI9jkHt2G -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -assembler spades -c C:\Users\albie\AppData\Local\Temp\T4hQOJX4w_ -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 8 tests of 8.
t/bin/eukaryote_assembly.t .........................................
Dubious, test returned 8 (wstat 2048, 0x800)
Failed 8/8 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\dVWhl2Oi2U -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\JKUKB2ns9M -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\uYBuhbMRJa -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\44LL5B1zt3 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\l1Ph3szZ8v -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\tDR9_0B6TH -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\9GZj3jktpv -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bwa -c C:\Users\albie\AppData\Local\Temp\4a5J8W8Mcu -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m smalt --smalt_index_k 15 --smalt_index_s 4 --smalt_mapper_r 1 --smalt_mapper_y 0.9 --smalt_mapper_x --smalt_mapper_l pe -c C:\Users\albie\AppData\Local\Temp\IWXoJU60oS -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m ssaha2 -c C:\Users\albie\AppData\Local\Temp\GoitYfTm5V -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\OjkRG7i5pW -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m tophat -c C:\Users\albie\AppData\Local\Temp\k6w2SjEVA8 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -p "StandardProtocol" -c C:\Users\albie\AppData\Local\Temp\d5PfBR8vZg -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\ck4nBatxyn -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 14 tests of 14.
t/bin/eukaryote_mapping.t ..........................................
Dubious, test returned 14 (wstat 3584, 0xe00)
Failed 14/14 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\6cW5OaAiAv -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -d some_other_db_name -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\rNA_Bd2AtB -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\1uBoCNvQuz -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\BK_hpdhnM2 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\PcYdKp2Wd_ -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\aSIRdB5EZQ -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\QwOx_m_qQM -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\qYzJIXWgXU -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 8 tests of 8.
t/bin/eukaryote_register_and_qc_study.t ............................
Dubious, test returned 8 (wstat 2048, 0x800)
Failed 8/8 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\Pbt6Tt9h3d -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\a3HPUQgfK7 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\9q1gly1Y6H -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\TvyUBfaFAY -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\H9W0XOXIhb -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\cH4YPxbqgx -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC --tophat_mapper_max_intron 10000 --tophat_mapper_min_intron 70 --tophat_mapper_max_multihit 1 -c C:\Users\albie\AppData\Local\Temp\6lGG3mcrBL -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\z692RHz3BS -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bwa -c C:\Users\albie\AppData\Local\Temp\QeNfMvwHEO -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m smalt -c C:\Users\albie\AppData\Local\Temp\GGWeLVuCmL -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m smalt --smalt_index_k 15 --smalt_index_s 4 --smalt_mapper_r 1 --smalt_mapper_y 0.9 --smalt_mapper_x -c C:\Users\albie\AppData\Local\Temp\lslwXArJId -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\vqhJwZ7iUg -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -p "StrandSpecificProtocol" -c C:\Users\albie\AppData\Local\Temp\2hf4Da4qIi -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\5P_9q5uKdA -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 14 tests of 14.
t/bin/eukaryote_rna_seq_expression.t ...............................
Dubious, test returned 14 (wstat 3584, 0xe00)
Failed 14/14 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\vx_svmRPry -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\WApZJVTRUt -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\4w8tdNry0R -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\dFYe1OAM2P -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\B3KTnZb7hj -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\GNbJZS8Z4c -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\sReGMM7XNB -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bwa -c C:\Users\albie\AppData\Local\Temp\D0wSLCFQ06 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m smalt --smalt_index_k 15 --smalt_index_s 4 --smalt_mapper_r 1 --smalt_mapper_y 0.9 --smalt_mapper_x -c C:\Users\albie\AppData\Local\Temp\ywfr_PId0v -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m ssaha2 -c C:\Users\albie\AppData\Local\Temp\EX2BpgkP9y -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\ggM1OHkfGI -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\F7nR8R31UY -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 12 tests of 12.
t/bin/eukaryote_snp_calling.t ......................................
Dubious, test returned 12 (wstat 3072, 0xc00)
Failed 12/12 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\ZDq8jabFND -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\mKAgTOZzHr -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\Uo0aBQ1EPZ -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\dBx8Ymv_ZG -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\MxUXsdS0Zi -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\uEZj5PLW_2 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\U1FkxeInTH -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bwa -c C:\Users\albie\AppData\Local\Temp\UCbnxpkDYs -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m smalt --smalt_index_k 15 --smalt_index_s 4 --smalt_mapper_r 1 --smalt_mapper_y 0.9 --smalt_mapper_x -c C:\Users\albie\AppData\Local\Temp\0OBcx9UeE1 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m ssaha2 -c C:\Users\albie\AppData\Local\Temp\5kJO2eeo2d -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\ozWnh70HVa -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m tophat -c C:\Users\albie\AppData\Local\Temp\OFgpEPKh1D -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -p "StandardProtocol" -c C:\Users\albie\AppData\Local\Temp\4WIwRjP_1q -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\Hs4xqp5IZE -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 14 tests of 14.
t/bin/helminth_mapping.t ...........................................
Dubious, test returned 14 (wstat 3584, 0xe00)
Failed 14/14 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\5Rp5DSRgbS -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -d some_other_db_name -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\trhdLByIxL -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\8okerMoffo -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\7ndUy7kVZ_ -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\jz3S8NxchN -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\S0cXYVU9Te -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\6BX6XkrTwD -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\cgWAzZG8yk -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 8 tests of 8.
t/bin/helminth_register_and_qc_study.t .............................
Dubious, test returned 8 (wstat 2048, 0x800)
Failed 8/8 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\KcFNa7hpxW -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\n8Ebhr287q -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\r1xFCDQqW8 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\yRT2YX_FQp -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\jGjYtt70qx -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\mVCaWKOg9M -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC --tophat_mapper_max_intron 10000 --tophat_mapper_min_intron 70 --tophat_mapper_max_multihit 1 -c C:\Users\albie\AppData\Local\Temp\twbpHES6GR -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\k3eCBXyVa7 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bwa -c C:\Users\albie\AppData\Local\Temp\NXD0WJ3H6k -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m smalt -c C:\Users\albie\AppData\Local\Temp\YlpuOxVFzB -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m smalt --smalt_index_k 15 --smalt_index_s 4 --smalt_mapper_r 1 --smalt_mapper_y 0.9 --smalt_mapper_x -c C:\Users\albie\AppData\Local\Temp\CUbOnBriic -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\9CQ8ebEYiu -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -p "StrandSpecificProtocol" -c C:\Users\albie\AppData\Local\Temp\Mz_HG2gaLD -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\vVin8Bn0iJ -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 14 tests of 14.
t/bin/helminth_rna_seq_expression.t ................................
Dubious, test returned 14 (wstat 3584, 0xe00)
Failed 14/14 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\JGJDoXy5Go -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\__XpGzwQHq -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\SGpqNFuHer -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\PbZXJUTXoo -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\2oZac6v9m0 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\4J5i3rEoSN -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\o6dxjedhp_ -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bwa -c C:\Users\albie\AppData\Local\Temp\0sXKEIZ_Hx -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m smalt --smalt_index_k 15 --smalt_index_s 4 --smalt_mapper_r 1 --smalt_mapper_y 0.9 --smalt_mapper_x -c C:\Users\albie\AppData\Local\Temp\GycbVI8i3C -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m ssaha2 -c C:\Users\albie\AppData\Local\Temp\Vw5xnFiwvE -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\pjGnKC248t -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\AQxDv4QH5d -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 12 tests of 12.
t/bin/helminth_snp_calling.t .......................................
Dubious, test returned 12 (wstat 3072, 0xc00)
Failed 12/12 subtests
# Failed test 'log file has been created for bacteria_assembly_and_annotation'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Unrecognized escape \U passed through in regex; marked by <-- HERE in m/^[\d]+ .+ \./bin/bacteria_assembly_and_annotation -c C:\U <-- HERE sers\albie\AppData\Local\Temp\Vx5_pBnqxY$/ at t/bin/log_parameters.t line 25.
Unrecognized escape \L passed through in regex; marked by <-- HERE in m/^[\d]+ .+ \./bin/bacteria_assembly_and_annotation -c C:\Users\albie\AppData\L <-- HERE ocal\Temp\Vx5_pBnqxY$/ at t/bin/log_parameters.t line 25.
Unrecognized escape \T passed through in regex; marked by <-- HERE in m/^[\d]+ .+ \./bin/bacteria_assembly_and_annotation -c C:\Users\albie\AppData\Local\T <-- HERE emp\Vx5_pBnqxY$/ at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for bacteria_assembly_single_cell'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Unrecognized escape \U passed through in regex; marked by <-- HERE in m/^[\d]+ .+ \./bin/bacteria_assembly_single_cell -c C:\U <-- HERE sers\albie\AppData\Local\Temp\2BtmsmGIk2$/ at t/bin/log_parameters.t line 25.
Unrecognized escape \L passed through in regex; marked by <-- HERE in m/^[\d]+ .+ \./bin/bacteria_assembly_single_cell -c C:\Users\albie\AppData\L <-- HERE ocal\Temp\2BtmsmGIk2$/ at t/bin/log_parameters.t line 25.
Unrecognized escape \T passed through in regex; marked by <-- HERE in m/^[\d]+ .+ \./bin/bacteria_assembly_single_cell -c C:\Users\albie\AppData\Local\T <-- HERE emp\2BtmsmGIk2$/ at t/bin/log_parameters.t line 25.
Reference to nonexistent group in regex; marked by <-- HERE in m/^[\d]+ .+ \./bin/bacteria_assembly_single_cell -c C:\Users\albie\AppData\Local\Temp\2 <-- HERE BtmsmGIk2$/ at t/bin/log_parameters.t line 25.
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 1 just after 3.
t/bin/log_parameters.t .............................................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 3/3 subtests
# Failed test 'files created as expected for ./bin/setup_global_configs -d pathogen_euk_track -c C:\Users\albie\AppData\Local\Temp\0K18zH8Pb7 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 25.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for ./bin/setup_global_configs -d some_other_db_name -c C:\Users\albie\AppData\Local\Temp\mrRhkDBy4v -l t/data/refs.index'
# at t/lib/TestHelper.pm line 25.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 2 tests of 2.
t/bin/setup_global_configs.t .......................................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/2 subtests
# Failed test 'files created as expected for -d some_other_db_name -t study -i ZZZ -c C:\Users\albie\AppData\Local\Temp\ITcJzKT7bB -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -c C:\Users\albie\AppData\Local\Temp\ywgXTP_ODC -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -c C:\Users\albie\AppData\Local\Temp\p600GSWHg8 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -c C:\Users\albie\AppData\Local\Temp\4KcNIa7qmz -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -c C:\Users\albie\AppData\Local\Temp\iRvncRrXNw -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -c C:\Users\albie\AppData\Local\Temp\AxhiFFRy6j -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -assembler velvet -c C:\Users\albie\AppData\Local\Temp\UFQTm1mP53 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\Pl22ud3nAQ -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 8 tests of 8.
t/bin/virus_assembly_and_annotation.t ..............................
Dubious, test returned 8 (wstat 2048, 0x800)
Failed 8/8 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\N9zwgnGrTX -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\OwZfWhfZc2 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\volkt8tezb -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\mFsTbNQtJ5 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\1v8YEcr9FM -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\lymJPXid_J -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\iWYzXPKEek -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bwa -c C:\Users\albie\AppData\Local\Temp\9r_H7hQZwK -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m ssaha2 -c C:\Users\albie\AppData\Local\Temp\dDfUVvmWSn -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\ZsZo47Feoy -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m tophat -c C:\Users\albie\AppData\Local\Temp\tZk8P8YO6F -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -p "StandardProtocol" -c C:\Users\albie\AppData\Local\Temp\xclWUsJGsi -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\eAOcmxcwRu -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 13 tests of 13.
t/bin/virus_mapping.t ..............................................
Dubious, test returned 13 (wstat 3328, 0xd00)
Failed 13/13 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\xbYxWKmqAW -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -d some_other_db_name -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\njx50D45_O -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\xNgfxjMfi7 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\a6f3gP88TF -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\dOQMlUWRO7 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\UKQlQctOx6 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\eXZiaK9YSp -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -assembler velvet -c C:\Users\albie\AppData\Local\Temp\d4m4l5aVov -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\loyaakOcBd -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 9 tests of 9.
t/bin/virus_register_and_qc_study.t ................................
Dubious, test returned 9 (wstat 2304, 0x900)
Failed 9/9 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\1lSYkJ8v7L -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\giimWFbS0A -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\aIcETH31ZE -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\2a3UKrqMjV -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\zIe7nDwukp -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\NWxTKeRji7 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\PAAoB0r7Da -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bwa -c C:\Users\albie\AppData\Local\Temp\SmjMHv_wfE -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\AXYR0nNR8k -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m tophat -c C:\Users\albie\AppData\Local\Temp\3DQPkUv9Pq -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -p "StandardProtocol" -c C:\Users\albie\AppData\Local\Temp\Qt6QRcrsMK -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\SYSzzaxU5f -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 12 tests of 12.
t/bin/virus_rna_seq_expression.t ...................................
Dubious, test returned 12 (wstat 3072, 0xc00)
Failed 12/12 subtests
# Failed test 'files created as expected for -a ABC -c C:\Users\albie\AppData\Local\Temp\9BBFAwjBo8 -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t file -i t/data/lanes_file -r ABC -c C:\Users\albie\AppData\Local\Temp\fhZWExosqt -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t lane -i 1234_5\#6 -r ABC -c C:\Users\albie\AppData\Local\Temp\33no1ZaSlN -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t library -i libname -r ABC -c C:\Users\albie\AppData\Local\Temp\vVhVk8aPce -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t sample -i sample -r ABC -c C:\Users\albie\AppData\Local\Temp\DX_ZdnCW0j -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -c C:\Users\albie\AppData\Local\Temp\SNqSMVW5LD -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bowtie2 -c C:\Users\albie\AppData\Local\Temp\zblUiwlgYG -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m bwa -c C:\Users\albie\AppData\Local\Temp\UoAwlqRSnf -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m ssaha2 -c C:\Users\albie\AppData\Local\Temp\XTiBAVWlfI -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -m stampy -c C:\Users\albie\AppData\Local\Temp\DoMP6htaOi -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for -t study -i ZZZ -r ABC -s Staphylococcus_aureus -c C:\Users\albie\AppData\Local\Temp\NbLkZGvZcN -l t/data/refs.index'
# at t/lib/TestHelper.pm line 55.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 11 tests of 11.
t/bin/virus_snp_calling.t ..........................................
Dubious, test returned 11 (wstat 2816, 0xb00)
Failed 11/11 subtests
The getpwuid function is unimplemented at lib/Bio/VertRes/Config/CommandLine/LogParameters.pm line 28.
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 1.
t/Bio/VertRes/Config/CommandLine/Common.t ..........................
Dubious, test returned 255 (wstat 65280, 0xff00)
All 1 subtests passed
t/Bio/VertRes/Config/CommandLine/ConstructLimits.t ................. ok
The getpwuid function is unimplemented at lib/Bio/VertRes/Config/CommandLine/LogParameters.pm line 28.
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 1.
t/Bio/VertRes/Config/CommandLine/LogParameters.t ...................
Dubious, test returned 255 (wstat 65280, 0xff00)
All 1 subtests passed
t/Bio/VertRes/Config/CommandLine/StudyNameSearch.t ................. ok
t/Bio/VertRes/Config/MultipleTopLevelFiles.t ....................... ok
t/Bio/VertRes/Config/Pipelines/AnnotateAssembly.t .................. ok
t/Bio/VertRes/Config/Pipelines/Assembly.t .......................... ok
t/Bio/VertRes/Config/Pipelines/BamImprovement.t .................... ok
t/Bio/VertRes/Config/Pipelines/Bowtie2Mapping.t .................... ok
t/Bio/VertRes/Config/Pipelines/BwaMapping.t ........................ ok
t/Bio/VertRes/Config/Pipelines/Common.t ............................ ok
t/Bio/VertRes/Config/Pipelines/Import.t ............................ ok
t/Bio/VertRes/Config/Pipelines/Mapping.t ........................... ok
t/Bio/VertRes/Config/Pipelines/QC.t ................................ ok
t/Bio/VertRes/Config/Pipelines/RnaSeqExpression.t .................. ok
t/Bio/VertRes/Config/Pipelines/SmaltMapping.t ...................... ok
t/Bio/VertRes/Config/Pipelines/SnpCalling.t ........................ ok
t/Bio/VertRes/Config/Pipelines/SpadesAssembly.t .................... ok
t/Bio/VertRes/Config/Pipelines/Ssaha2Mapping.t ..................... ok
t/Bio/VertRes/Config/Pipelines/StampyMapping.t ..................... ok
t/Bio/VertRes/Config/Pipelines/Store.t ............................. ok
t/Bio/VertRes/Config/Pipelines/Tradis.t ............................ ok
t/Bio/VertRes/Config/Pipelines/VelvetAssembly.t .................... ok
t/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.t ....... ok
t/Bio/VertRes/Config/Recipes/BacteriaAssemblySingleCell.t .......... ok
t/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.t .......... ok
t/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingBwa.t .... ok
t/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingSmalt.t .. ok
t/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingBwa.t .......... ok
t/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingSmalt.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesAssembly.t .................. ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingBwa.t ........... ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSmalt.t ......... ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSsaha2.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingStampy.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesRegisterAndQCStudy.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesRnaSeqExpression.t .......... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingBwa.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSmalt.t ...... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSsaha2.t ..... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingStampy.t ..... ok
t/Bio/VertRes/Config/Recipes/Global.t .............................. ok
t/Bio/VertRes/Config/Recipes/HelminthRegisterAndQCStudy.t .......... ok
t/Bio/VertRes/Config/Recipes/VirusAssemblyAndAnnotation.t .......... ok
t/Bio/VertRes/Config/Recipes/VirusRegisterAndQCStudy.t ............. ok
t/Bio/VertRes/Config/References.t .................................. ok
t/Bio/VertRes/Config/RegisterStudy.t ............................... ok
t/Bio/VertRes/Config/TopLevel.t .................................... ok
Test Summary Report
-------------------
t/bin/bacteria_assembly_and_annotation.t (Wstat: 2048 Tests: 8 Failed: 8)
Failed tests: 1-8
Non-zero exit status: 8
t/bin/bacteria_assembly_single_cell.t (Wstat: 1536 Tests: 6 Failed: 6)
Failed tests: 1-6
Non-zero exit status: 6
t/bin/bacteria_mapping.t (Wstat: 3328 Tests: 13 Failed: 13)
Failed tests: 1-13
Non-zero exit status: 13
t/bin/bacteria_register_and_qc_study.t (Wstat: 2304 Tests: 9 Failed: 9)
Failed tests: 1-9
Non-zero exit status: 9
t/bin/bacteria_rna_seq_expression.t (Wstat: 3072 Tests: 12 Failed: 12)
Failed tests: 1-12
Non-zero exit status: 12
t/bin/bacteria_snp_calling.t (Wstat: 2816 Tests: 11 Failed: 11)
Failed tests: 1-11
Non-zero exit status: 11
t/bin/eukaryote_assembly.t (Wstat: 2048 Tests: 8 Failed: 8)
Failed tests: 1-8
Non-zero exit status: 8
t/bin/eukaryote_mapping.t (Wstat: 3584 Tests: 14 Failed: 14)
Failed tests: 1-14
Non-zero exit status: 14
t/bin/eukaryote_register_and_qc_study.t (Wstat: 2048 Tests: 8 Failed: 8)
Failed tests: 1-8
Non-zero exit status: 8
t/bin/eukaryote_rna_seq_expression.t (Wstat: 3584 Tests: 14 Failed: 14)
Failed tests: 1-14
Non-zero exit status: 14
t/bin/eukaryote_snp_calling.t (Wstat: 3072 Tests: 12 Failed: 12)
Failed tests: 1-12
Non-zero exit status: 12
t/bin/helminth_mapping.t (Wstat: 3584 Tests: 14 Failed: 14)
Failed tests: 1-14
Non-zero exit status: 14
t/bin/helminth_register_and_qc_study.t (Wstat: 2048 Tests: 8 Failed: 8)
Failed tests: 1-8
Non-zero exit status: 8
t/bin/helminth_rna_seq_expression.t (Wstat: 3584 Tests: 14 Failed: 14)
Failed tests: 1-14
Non-zero exit status: 14
t/bin/helminth_snp_calling.t (Wstat: 3072 Tests: 12 Failed: 12)
Failed tests: 1-12
Non-zero exit status: 12
t/bin/log_parameters.t (Wstat: 256 Tests: 3 Failed: 3)
Failed tests: 1-3
Non-zero exit status: 1
Parse errors: No plan found in TAP output
t/bin/setup_global_configs.t (Wstat: 512 Tests: 2 Failed: 2)
Failed tests: 1-2
Non-zero exit status: 2
t/bin/virus_assembly_and_annotation.t (Wstat: 2048 Tests: 8 Failed: 8)
Failed tests: 1-8
Non-zero exit status: 8
t/bin/virus_mapping.t (Wstat: 3328 Tests: 13 Failed: 13)
Failed tests: 1-13
Non-zero exit status: 13
t/bin/virus_register_and_qc_study.t (Wstat: 2304 Tests: 9 Failed: 9)
Failed tests: 1-9
Non-zero exit status: 9
t/bin/virus_rna_seq_expression.t (Wstat: 3072 Tests: 12 Failed: 12)
Failed tests: 1-12
Non-zero exit status: 12
t/bin/virus_snp_calling.t (Wstat: 2816 Tests: 11 Failed: 11)
Failed tests: 1-11
Non-zero exit status: 11
t/Bio/VertRes/Config/CommandLine/Common.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/Bio/VertRes/Config/CommandLine/LogParameters.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
Files=70, Tests=747, 106 wallclock secs ( 0.44 usr + 0.11 sys = 0.55 CPU)
Result: FAIL
Failed 24/70 test programs. 221/747 subtests failed.
dmake.exe: Error code 255, while making 'test_dynamic'
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------------- ---- -------
Data::Dumper 0 2.151
DBI 0 1.631
Exception::Class 0 1.38
File::Basename 0 2.85
File::Path 0 2.09
File::Slurp 0 9999.19
Getopt::Long 0 2.42
Moose 0 2.1403
Moose::Role 0 2.1403
Moose::Util::TypeConstraints 0 2.1403
build_requires:
Module Need Have
---------------------------- ---- -------
File::Find 0 1.27
File::Temp 0 0.2304
strict 0 1.08
Test::Most 0 0.33
warnings 0 1.23
configure_requires:
Module Need Have
---------------------------- ---- -------
ExtUtils::MakeMaker 6.30 6.98
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
COMSPEC = C:\Windows\system32\cmd.exe
NUMBER_OF_PROCESSORS = 1
PATH = C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Strawberry\c\bin;C:\Strawberry\perl\site\bin;C:\Strawberry\perl\bin;C:\Program Files\Git\cmd
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 2456
PERL5_CPAN_IS_RUNNING = 2456
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 2996,2456
PERL_CR_SMOKER_CURRENT = Bio-VertRes-Config-1.133090
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
PROCESSOR_IDENTIFIER = x86 Family 21 Model 1 Stepping 2, AuthenticAMD
TEMP = C:\Users\albie\AppData\Local\Temp
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = C:\Strawberry\perl\bin\perl.exe
$UID/$EUID = 0 / 0
$GID = 0
$EGID = 0
Win32::GetOSName = Win7
Win32::GetOSVersion = Service Pack 1, 6, 1, 7601, 2, 1, 0, 256, 1
Win32::FsType = NTFS
Win32::IsAdminUser = 0
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.05
CPAN::Meta 2.143240
Cwd 3.47
ExtUtils::CBuilder 0.280216
ExtUtils::Command 1.18
ExtUtils::Install 1.68
ExtUtils::MakeMaker 6.98
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.24
File::Spec 3.47
JSON 2.90
JSON::PP 2.27203
Module::Build 0.4205
Module::Signature n/a
Parse::CPAN::Meta 1.4414
Test::Harness 3.32
Test::More 1.001003
YAML 0.94
YAML::Syck 1.27
version 0.9908
--
Summary of my perl5 (revision 5 version 20 subversion 0) configuration:
Platform:
osname=MSWin32, osvers=6.2, archname=MSWin32-x86-multi-thread-64int
uname='Win32 strawberry-perl 5.20.0.1 #1 Fri May 30 23:25:11 2014 i386'
config_args='undef'
hint=recommended, useposix=true, d_sigaction=undef
useithreads=define, usemultiplicity=define
use64bitint=define, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='gcc', ccflags =' -s -O2 -DWIN32 -DPERL_TEXTMODE_SCRIPTS -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -DUSE_PERLIO -fwrapv -fno-strict-aliasing -mms-bitfields',
optimize='-s -O2',
cppflags='-DWIN32'
ccversion='', gccversion='4.8.2', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long long', ivsize=8, nvtype='double', nvsize=8, Off_t='long long', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='g++', ldflags ='-s -L"C:\STRAWB~1\perl\lib\CORE" -L"C:\STRAWB~1\c\lib"'
libpth=C:\STRAWB~1\c\lib C:\STRAWB~1\c\i686-w64-mingw32\lib C:\STRAWB~1\c\lib\gcc\i686-w64-mingw32\4.8.2
libs=-lmoldname -lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvapi32 -lshell32 -lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lversion -lodbc32 -lodbccp32 -lcomctl32
perllibs=-lmoldname -lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvapi32 -lshell32 -lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lversion -lodbc32 -lodbccp32 -lcomctl32
libc=, so=dll, useshrplib=true, libperl=libperl520.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_win32.xs, dlext=xs.dll, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags='-mdll -s -L"C:\STRAWB~1\perl\lib\CORE" -L"C:\STRAWB~1\c\lib"'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES HAVE_INTERP_INTERN MULTIPLICITY
PERLIO_LAYERS PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_IMPLICIT_SYS
PERL_MALLOC_WRAP PERL_NEW_COPY_ON_WRITE
PERL_PRESERVE_IVUV USE_64_BIT_INT USE_ITHREADS
USE_LARGE_FILES USE_LOCALE USE_LOCALE_COLLATE
USE_LOCALE_CTYPE USE_LOCALE_NUMERIC USE_PERLIO
USE_PERL_ATOF
Built under MSWin32
Compiled at May 30 2014 23:29:27
%ENV:
PERL5_CPANPLUS_IS_RUNNING="2456"
PERL5_CPAN_IS_RUNNING="2456"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="2996,2456"
PERL_CR_SMOKER_CURRENT="Bio-VertRes-Config-1.133090"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
C:/Strawberry/perl/site/lib/MSWin32-x86-multi-thread-64int
C:/Strawberry/perl/site/lib
C:/Strawberry/perl/vendor/lib
C:/Strawberry/perl/lib
.