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chadlaing / Panseq

Pan-genomic sequence analysis
http://lfz.corefacility.ca/panseq
GNU General Public License v3.0
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test fails for 6 genomes #9

Closed hpourreza closed 7 years ago

hpourreza commented 8 years ago

I am not sure if this is the best place to post but I did not find any mailing list, etc. to ask this question.

I installed Panseq and all its prerequisites. When I try to run the test, it fails for 6 genomes:

Settings file: t/genomes.batch 2016/06/09 09:15:51 INFO | NovelIterator.pm:186> We have 6 genomes this run 2016/06/09 09:16:26 INFO | Panseq.pm:253> Panseq mode set as pan 2016/06/09 09:16:26 INFO | SegmentMaker.pm:164> Segmenting t/genomes/5cab9e25afd603ac843befcc870cc3be_9cfa6d9cba95e7e695ff73dc8e834bfe into 1000bp segments 2016/06/09 09:16:28 INFO | FastaFileSplitter.pm:127> Splitting t/genomes/pangenome_fragments.fasta into 1 files 2016/06/09 09:16:29 INFO | PanGenome.pm:208> Analyzing the pan-genome 2016/06/09 09:16:29 INFO | PanGenome.pm:213> Processing Blast output files 2016/06/09 09:16:29 FATAL | BlastResults.pm:62> No such file or directory 2016/06/09 09:16:30 WARN | CombineFilesIntoSingleFile.pm:82> Skipping t/genomes/1_coreGenomeFragments as it has size of 0 2016/06/09 09:16:30 WARN | CombineFilesIntoSingleFile.pm:82> Skipping t/genomes/1_accessoryGenomeFragments as it has size of 0 2016/06/09 09:16:30 WARN | CombineFilesIntoSingleFile.pm:82> Skipping t/genomes/1_locus_alleles as it has size of 0 2016/06/09 09:16:30 INFO | PanGenome.pm:301> Processing blast output files complete 2016/06/09 09:16:30 INFO | PanGenome.pm:302> Pan-genome generation complete 2016/06/09 09:16:30 INFO | Panseq.pm:458> Creating zip file ✖ plasmidsCoreSnps generated correctly Failed test 'plasmidsCoreSnps generated correctly' at t/output.t line 154. got: '74159081ba92c9866cab796d6180f3d9' expected: 'a7d2902d80543446a6701e8f8770301b' ✖ plasmidsPanGenome generated correctly Failed test 'plasmidsPanGenome generated correctly' at t/output.t line 155. got: '74159081ba92c9866cab796d6180f3d9' expected: '168d75b59dbe825cd91222906a4f5645'

and many lines similar to the above

I am using Perl 5.22.1 on CentOS 6.6. mummer 3.23, muscle 3.8.31, and blast+ 2.3.0

Any advice will be greatly appreciated.

chadlaing commented 8 years ago

Hi,

Are the program locations different from the following?

blastDirectory = '/usr/bin/'
mummerDirectory = '/usr/bin/'
muscleExecutable = '/usr/bin/muscle'
hpourreza commented 8 years ago

Yes they are and I have --blastDrirectory etc. when I run the test program.

chadlaing commented 8 years ago

Hi,

I have discovered the problem. NCBI has changed BLAST+ slightly since the 2.2.29 release, which produces non-identical output, and causes the tests to fail. I will update the tests in the future to take into account the BLAST+ version, but for now to ensure a correct installation, download the 2.2.29 release from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/

hpourreza commented 8 years ago

Many thanks

gsong1205 commented 8 years ago

still have this problem after installing blast+2.2.9

chadlaing commented 8 years ago

Could you post the output of the test run?

gsong1205 commented 8 years ago

Failed test 'plasmidsCoreSnps generated correctly' Failed test 'plasmidsSnpTable generated correctly' Failed test 'queryCoreSnps generated correctly' Failed test 'genomesSnpTable generated correctly' Failed test 'querySnpTable generated correctly' Failed test 'genomesSnpPhylip generated correctly'

gsong1205 commented 8 years ago

Like this: not ok 22 - genomesSnpPhylip generated correctly

Failed test 'genomesSnpPhylip generated correctly'

at t/output.t line 168.

+-----------+--------------------------+----+--------------------------+

| PATH | GOT | OP | CHECK |

+-----------+--------------------------+----+--------------------------+

| <Check 0> | 58b81557c3ac31d51b85256b | eq | f438ce263872f10b36cb3247 |

| | 38c247da | | a3d5dd59 |

| | | | |

| <Check 1> | 58b81557c3ac31d51b85256b | eq | 309eb8bce6de7737a4de7991 |

| | 38c247da | | 31a2b4e3 |

| | | | |

| <Check 2> | 58b81557c3ac31d51b85256b | eq | 11966e574aacd819e8e610d3 |

| | 38c247da | | 628c3fac |

+-----------+--------------------------+----+--------------------------+

ok 23 - genomesBinaryPhylip generated correctly ok 24 - genomesNameConversion generated correctly ok 25 - genomesAccessoryFragments generated correctly ok 26 - genomesCoreFragments generated correctly

chadlaing commented 8 years ago

what is the output of git rev-parse HEAD? in the Panseq directory?

gsong1205 commented 8 years ago

the output is c7b3abda1757a130373070e32027436dfa3c8896

gsong1205 commented 8 years ago

c 7 b 3 a b d a 1 7 57a130373070e32027436dfa3c8896

gsong1205 commented 8 years ago

any progress?

chadlaing commented 8 years ago

does this still happen with BLAST+ 2.2.29 for you?

gsong1205 commented 8 years ago

yes. Still the same problem.

chadlaing commented 8 years ago

could you run the following:

perl t/output.t --type plasmids --removeRun 0 > testoutput.txt

And then email the testoutput.txt and t/plasmids/Master.log files to chad.laing@canada.ca?

chadlaing commented 8 years ago

Hi,

Can you try changing muscleExecutable from a directory name to the actual muscle program file name and see if that solves the problem?

Thanks

gsong1205 commented 8 years ago

It works!!!!!!! Thank you so much!!!!

chadlaing commented 8 years ago

No problem, I'm glad it works.

glichtenstein commented 7 years ago

Hello @chadlaing ,

After installing Panseq, I encounter a very similar issue as reported by @gsong1205 :

I am running:

perl t/output.t \
--blastDirectory '/share/apps/ncbi-blast-2.2.29+/bin/' \
--mummerDirectory '/share/apps/MUMmer/' \
--cdhitDirectory '/share/apps/cdhit/' \
--muscleExecutable '/share/apps/muscle/muscle3.8.31_i86linux64' \
--type plasmids \
--removeRun 0 \
> testoutput.txt

and it resulted in:

> # Failed test 'plasmidsCoreSnps generated correctly'
> # at t/output.t line 221.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | b3db8e082b4e80082e6fe028 | eq | a7d2902d80543446a6701e8f |
> # |           | 5934807b                 |    | 8770301b                 |
> # |           |                          |    |                          |
> # | <Check 1> | b3db8e082b4e80082e6fe028 | eq | 1a7a78da13820f54bb619a4d |
> # |           | 5934807b                 |    | f0f2df2f                 |
> # |           |                          |    |                          |
> # | <Check 2> | b3db8e082b4e80082e6fe028 | eq | 1133816b845a5391f552e8e6 |
> # |           | 5934807b                 |    | 0b0eed8b                 |
> # |           |                          |    |                          |
> # | <Check 3> | b3db8e082b4e80082e6fe028 | eq | 388ad37fe11273ece738664f |
> # |           | 5934807b                 |    | d00ae121                 |
> # |           |                          |    |                          |
> # | <Check 4> | b3db8e082b4e80082e6fe028 | eq | 943a1cf71152037cb1543b0c |
> # |           | 5934807b                 |    | acec2fff                 |
> # |           |                          |    |                          |
> # | <Check 5> | b3db8e082b4e80082e6fe028 | eq | 4c34b6ea16f000281413a51e |
> # |           | 5934807b                 |    | 7f1a96cc                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'plasmidsPanGenome generated correctly'
> # at t/output.t line 222.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | ceb9ccdb9e9d6c1d305a9473 | eq | 168d75b59dbe825cd9122290 |
> # |           | 00095531                 |    | 6a4f5645                 |
> # |           |                          |    |                          |
> # | <Check 1> | ceb9ccdb9e9d6c1d305a9473 | eq | de611f27d9691d4f2e798007 |
> # |           | 00095531                 |    | ab49583a                 |
> # |           |                          |    |                          |
> # | <Check 2> | ceb9ccdb9e9d6c1d305a9473 | eq | e60ab1fb4adaf0e13ac342a4 |
> # |           | 00095531                 |    | 82cc4a96                 |
> # |           |                          |    |                          |
> # | <Check 3> | ceb9ccdb9e9d6c1d305a9473 | eq | 35c7ee30137ccf2737b6e171 |
> # |           | 00095531                 |    | 7149620c                 |
> # |           |                          |    |                          |
> # | <Check 4> | ceb9ccdb9e9d6c1d305a9473 | eq | 18b07b36e448492ac162624e |
> # |           | 00095531                 |    | 36628444                 |
> # |           |                          |    |                          |
> # | <Check 5> | ceb9ccdb9e9d6c1d305a9473 | eq | 6674c78f04dcbe10b569e247 |
> # |           | 00095531                 |    | 990e27b5                 |
> # |           |                          |    |                          |
> # | <Check 6> | ceb9ccdb9e9d6c1d305a9473 | eq | a5c4a6fefc6977063c136e01 |
> # |           | 00095531                 |    | 26a6e2c9                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'plasmidsBinaryTable generated correctly'
> # at t/output.t line 223.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | 68fc51fd11a46c4c9b957a38 | eq | fbfffe4e58a1dfc1cd04cb29 |
> # |           | d1f0b7e3                 |    | b5146c0d                 |
> # |           |                          |    |                          |
> # | <Check 1> | 68fc51fd11a46c4c9b957a38 | eq | 387d3415808e3ed9ef0ffa60 |
> # |           | d1f0b7e3                 |    | c6b7fd67                 |
> # |           |                          |    |                          |
> # | <Check 2> | 68fc51fd11a46c4c9b957a38 | eq | 9524c956d024e323de747623 |
> # |           | d1f0b7e3                 |    | b67871e1                 |
> # |           |                          |    |                          |
> # | <Check 3> | 68fc51fd11a46c4c9b957a38 | eq | facdac694c0f7f8603f74151 |
> # |           | d1f0b7e3                 |    | cdefd7a6                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'plasmidsSnpTable generated correctly'
> # at t/output.t line 224.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | ad9ee36bfc01d4fe2feec017 | eq | 188356ccf7f73066c333e82d |
> # |           | ea3c97ea                 |    | d18e531d                 |
> # |           |                          |    |                          |
> # | <Check 1> | ad9ee36bfc01d4fe2feec017 | eq | 2e69ced50fb7d1f13e84e00d |
> # |           | ea3c97ea                 |    | fdbd2b5a                 |
> # |           |                          |    |                          |
> # | <Check 2> | ad9ee36bfc01d4fe2feec017 | eq | b8624a47c1edc7193d01a8b0 |
> # |           | ea3c97ea                 |    | 7c039e27                 |
> # |           |                          |    |                          |
> # | <Check 3> | ad9ee36bfc01d4fe2feec017 | eq | 5e03e2cdc49d4d4d1a33cf12 |
> # |           | ea3c97ea                 |    | 4f192ee2                 |
> # |           |                          |    |                          |
> # | <Check 4> | ad9ee36bfc01d4fe2feec017 | eq | 883396f6d5f8d5d5918777a0 |
> # |           | ea3c97ea                 |    | a4ee6e97                 |
> # |           |                          |    |                          |
> # | <Check 5> | ad9ee36bfc01d4fe2feec017 | eq | 92a15888a3beee351cebc433 |
> # |           | ea3c97ea                 |    | 02457824                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'plasmidsSnpPhylip generated correctly'
> # at t/output.t line 225.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | b8d30626c5f6eab98e960dc8 | eq | 6c8f15448b0f19be9efbb79e |
> # |           | 3f1df680                 |    | 16256350                 |
> # |           |                          |    |                          |
> # | <Check 1> | b8d30626c5f6eab98e960dc8 | eq | 4ae7de5409064454c0b8c17d |
> # |           | 3f1df680                 |    | 47cd10c8                 |
> # |           |                          |    |                          |
> # | <Check 2> | b8d30626c5f6eab98e960dc8 | eq | 52b8a7b0e45e8e0ccdcddebd |
> # |           | 3f1df680                 |    | 47e4c3a4                 |
> # |           |                          |    |                          |
> # | <Check 3> | b8d30626c5f6eab98e960dc8 | eq | 922767f0f9205ea242303ee7 |
> # |           | 3f1df680                 |    | 66014624                 |
> # |           |                          |    |                          |
> # | <Check 4> | b8d30626c5f6eab98e960dc8 | eq | 2ca6ba039d01c1ca0cf4bae1 |
> # |           | 3f1df680                 |    | 1bd07cfc                 |
> # |           |                          |    |                          |
> # | <Check 5> | b8d30626c5f6eab98e960dc8 | eq | d490e061720aa36303cb3acb |
> # |           | 3f1df680                 |    | f55b4bb3                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'plasmidsBinaryPhylip generated correctly'
> # at t/output.t line 226.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | f67ca4c2b4a0e8e8da84ed1d | eq | db5e15a38d9b7b7be53811df |
> # |           | f87e330e                 |    | 302d7558                 |
> # |           |                          |    |                          |
> # | <Check 1> | f67ca4c2b4a0e8e8da84ed1d | eq | b418d9d4a7c404ba859a40b2 |
> # |           | f87e330e                 |    | 540a30ec                 |
> # |           |                          |    |                          |
> # | <Check 2> | f67ca4c2b4a0e8e8da84ed1d | eq | 210104cefd498b805d040ae7 |
> # |           | f87e330e                 |    | 89e81f52                 |
> # |           |                          |    |                          |
> # | <Check 3> | f67ca4c2b4a0e8e8da84ed1d | eq | fd0779e2c1cacef90fbf5594 |
> # |           | f87e330e                 |    | a52cf8a6                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'plasmidsAccessoryFragments generated correctly'
> # at t/output.t line 233.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | 314ffb75540ebd38a9d06aba | eq | f17e29fd8ca3dbaac3033ce1 |
> # |           | 76518f4c                 |    | 88018465                 |
> # |           |                          |    |                          |
> # | <Check 1> | 314ffb75540ebd38a9d06aba | eq | 3c853ac88d7ea51c757b60fc |
> # |           | 76518f4c                 |    | 9edda08f                 |
> # |           |                          |    |                          |
> # | <Check 2> | 314ffb75540ebd38a9d06aba | eq | 203f613ce413cc2e97f15134 |
> # |           | 76518f4c                 |    | ae3fe627                 |
> # |           |                          |    |                          |
> # | <Check 3> | 314ffb75540ebd38a9d06aba | eq | 399c70234d36995e76602614 |
> # |           | 76518f4c                 |    | 94255098                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'plasmidsCoreFragments generated correctly'
> # at t/output.t line 234.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | 91274018bf2174a2130f4ee9 | eq | 2fa21523c2c0e9abde0836f2 |
> # |           | 17c9fa1e                 |    | a754640e                 |
> # |           |                          |    |                          |
> # | <Check 1> | 91274018bf2174a2130f4ee9 | eq | ba16baa4bf8786d2d6ab961f |
> # |           | 17c9fa1e                 |    | 6bff4c54                 |
> # |           |                          |    |                          |
> # | <Check 2> | 91274018bf2174a2130f4ee9 | eq | bd5e19b696e6ef5602c3456e |
> # |           | 17c9fa1e                 |    | 2792b493                 |
> # |           |                          |    |                          |
> # | <Check 3> | 91274018bf2174a2130f4ee9 | eq | a277c0f894016404a5570adb |
> # |           | 17c9fa1e                 |    | 5236c35f                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'queryCoreSnps generated correctly'
> # at t/output.t line 221.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | ebf3da78edea7128a30cefbf | eq | 67daf16fc332d162e485227f |
> # |           | dadd4c30                 |    | 80e22958                 |
> # |           |                          |    |                          |
> # | <Check 1> | ebf3da78edea7128a30cefbf | eq | 7165a8f1e22caa04c962cf60 |
> # |           | dadd4c30                 |    | 78cfb9c5                 |
> # |           |                          |    |                          |
> # | <Check 2> | ebf3da78edea7128a30cefbf | eq | 30665146a5839420ffd69825 |
> # |           | dadd4c30                 |    | 5be4d525                 |
> # |           |                          |    |                          |
> # | <Check 3> | ebf3da78edea7128a30cefbf | eq | 38cc7d3b5313b70da96e88f5 |
> # |           | dadd4c30                 |    | 922b079f                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'queryPanGenome generated correctly'
> # at t/output.t line 222.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | d73c4fe4a60349b461d69820 | eq | a603a5526709da34bc854363 |
> # |           | 22694ce5                 |    | 045c94bf                 |
> # |           |                          |    |                          |
> # | <Check 1> | d73c4fe4a60349b461d69820 | eq | 08d5efc3dabe27ce8a20b4eb |
> # |           | 22694ce5                 |    | a47cce87                 |
> # |           |                          |    |                          |
> # | <Check 2> | d73c4fe4a60349b461d69820 | eq | 65a31e3da4d40660a8d10860 |
> # |           | 22694ce5                 |    | fcac088f                 |
> # |           |                          |    |                          |
> # | <Check 3> | d73c4fe4a60349b461d69820 | eq | 70fd3f4d318d2652547b9d7c |
> # |           | 22694ce5                 |    | 392572c7                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'queryBinaryTable generated correctly'
> # at t/output.t line 223.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | d5c8936e9e4717e43debdb8b | eq | 1727cd2ef07eb60827937175 |
> # |           | 95e60433                 |    | 21d7146f                 |
> # |           |                          |    |                          |
> # | <Check 1> | d5c8936e9e4717e43debdb8b | eq | 527c728e651b3c29826ac251 |
> # |           | 95e60433                 |    | 9f5b73ed                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'querySnpTable generated correctly'
> # at t/output.t line 224.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | b9b7a7fa475c6d1425b04727 | eq | aca086386f540630499b24f0 |
> # |           | 1dd52813                 |    | e3644e3d                 |
> # |           |                          |    |                          |
> # | <Check 1> | b9b7a7fa475c6d1425b04727 | eq | 5534705c6b68cba9efdfa861 |
> # |           | 1dd52813                 |    | d5726ea3                 |
> # |           |                          |    |                          |
> # | <Check 2> | b9b7a7fa475c6d1425b04727 | eq | 3c15986290bca6b6b10ca42e |
> # |           | 1dd52813                 |    | e9236446                 |
> # |           |                          |    |                          |
> # | <Check 3> | b9b7a7fa475c6d1425b04727 | eq | 94665e9192961eb0cb828b0d |
> # |           | 1dd52813                 |    | d74bdc68                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'querySnpPhylip generated correctly'
> # at t/output.t line 225.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | 8a735ed9ea8425b35daf9d95 | eq | 972f68dff31780ddab9c1ac8 |
> # |           | 3bc8c170                 |    | 7b78eddd                 |
> # |           |                          |    |                          |
> # | <Check 1> | 8a735ed9ea8425b35daf9d95 | eq | e80e1aeb58dfba9d6680fac7 |
> # |           | 3bc8c170                 |    | 4c435e68                 |
> # |           |                          |    |                          |
> # | <Check 2> | 8a735ed9ea8425b35daf9d95 | eq | 8e77f99d3d9ab08b6137308a |
> # |           | 3bc8c170                 |    | e8b670b2                 |
> # |           |                          |    |                          |
> # | <Check 3> | 8a735ed9ea8425b35daf9d95 | eq | edc9bbe9e0b80c7345fe7b71 |
> # |           | 3bc8c170                 |    | 0c723e3b                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'queryBinaryPhylip generated correctly'
> # at t/output.t line 226.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | 04634f16509ea64bf1651502 | eq | 183fea98a21e4f9eae54e486 |
> # |           | b28f4b78                 |    | f1f08821                 |
> # |           |                          |    |                          |
> # | <Check 1> | 04634f16509ea64bf1651502 | eq | 1c25ac9ce8d7b3b2e9df4a7f |
> # |           | b28f4b78                 |    | 0318ec95                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'queryAlleles generated correctly'
> # at t/output.t line 229.
> # +-----------+--------------------------+----+--------------------------+
> # | PATH      | GOT                      | OP | CHECK                    |
> # +-----------+--------------------------+----+--------------------------+
> # | <Check 0> | 4907486a5afd20010d96feb5 | eq | 7aec36d7ee53447e0dd5e82b |
> # |           | 3c778825                 |    | e3d2f9bc                 |
> # |           |                          |    |                          |
> # | <Check 1> | 4907486a5afd20010d96feb5 | eq | 75d9944105a3ed95041024c6 |
> # |           | 3c778825                 |    | 0e9202cc                 |
> # |           |                          |    |                          |
> # | <Check 2> | 4907486a5afd20010d96feb5 | eq | dcd9041f5aa586ce8c0b0474 |
> # |           | 3c778825                 |    | 6cf2da62                 |
> # |           |                          |    |                          |
> # | <Check 3> | 4907486a5afd20010d96feb5 | eq | 1c73f71e9da53e2d55f1645b |
> # |           | 3c778825                 |    | 0a074dc6                 |
> # +-----------+--------------------------+----+--------------------------+
> # Failed test 'sha1CoreSnps generated correctly'
> # at t/output.t line 221.
> # +--------------------------------+----+--------------------------------+
> # | GOT                            | OP | CHECK                          |
> # +--------------------------------+----+--------------------------------+
> # | ec3fb19eb3b5e538d6ab4872c2571d | eq | 943a1cf71152037cb1543b0cacec2f |
> # | 03                             |    | ff                             |
> # +--------------------------------+----+--------------------------------+
> # Failed test 'sha1PanGenome generated correctly'
> # at t/output.t line 222.
> # +--------------------------------+----+--------------------------------+
> # | GOT                            | OP | CHECK                          |
> # +--------------------------------+----+--------------------------------+
> # | e766d4031dfe1660e884fd7e5a3de8 | eq | 6674c78f04dcbe10b569e247990e27 |
> # | 18                             |    | b5                             |
> # +--------------------------------+----+--------------------------------+
> # Failed test 'sha1BinaryTable generated correctly'
> # at t/output.t line 223.
> # +--------------------------------+----+--------------------------------+
> # | GOT                            | OP | CHECK                          |
> # +--------------------------------+----+--------------------------------+
> # | 94f1901907aa8e8232b8e53706b51e | eq | 9524c956d024e323de747623b67871 |
> # | 72                             |    | e1                             |
> # +--------------------------------+----+--------------------------------+
> # Failed test 'sha1SnpTable generated correctly'
> # at t/output.t line 224.
> # +--------------------------------+----+--------------------------------+
> # | GOT                            | OP | CHECK                          |
> # +--------------------------------+----+--------------------------------+
> # | a802f63c56f6095ca30327fd9ff997 | eq | 883396f6d5f8d5d5918777a0a4ee6e |
> # | c5                             |    | 97                             |
> # +--------------------------------+----+--------------------------------+
> # Failed test 'sha1SnpPhylip generated correctly'
> # at t/output.t line 225.
> # +--------------------------------+----+--------------------------------+
> # | GOT                            | OP | CHECK                          |
> # +--------------------------------+----+--------------------------------+
> # | 77489654d0ceb421c81184e410c4e7 | eq | 2ca6ba039d01c1ca0cf4bae11bd07c |
> # | ee                             |    | fc                             |
> # +--------------------------------+----+--------------------------------+
> # Failed test 'sha1BinaryPhylip generated correctly'
> # at t/output.t line 226.
> # +--------------------------------+----+--------------------------------+
> # | GOT                            | OP | CHECK                          |
> # +--------------------------------+----+--------------------------------+
> # | 9f28add01b4dbf27223e620159d854 | eq | 210104cefd498b805d040ae789e81f |
> # | 89                             |    | 52                             |
> # +--------------------------------+----+--------------------------------+
> # Failed test 'sha1AccessoryFragments generated correctly'
> # at t/output.t line 233.
> # +--------------------------------+----+--------------------------------+
> # | GOT                            | OP | CHECK                          |
> # +--------------------------------+----+--------------------------------+
> # | f702aa2874a0c8159efc474f8e2f02 | eq | 203f613ce413cc2e97f15134ae3fe6 |
> # | 99                             |    | 27                             |
> # +--------------------------------+----+--------------------------------+
> # Failed test 'sha1CoreFragments generated correctly'
> # at t/output.t line 234.
> # +--------------------------------+----+--------------------------------+
> # | GOT                            | OP | CHECK                          |
> # +--------------------------------+----+--------------------------------+
> # | 1640e17e2b687f8c5100546c281ccf | eq | bd5e19b696e6ef5602c3456e2792b4 |
> # | d4                             |    | 93                             |
> # +--------------------------------+----+--------------------------------+
> # Did not follow plan: expected 35, ran 26.
>

I am attaching the testoutput.txt,

any help would be much appreciated,

Thank you very much,

BRGDS,

Gabriel testoutput.txt

chadlaing commented 7 years ago

Hi,

I see blast+ 2.2.29 so I will take a look.

Thanks, Chad

chadlaing commented 7 years ago

All tests pass with blast+ 2.2.29 on my machine. I notice that in the output, 8 cores are being used. For the tests, everything should run single core to ensure identical output for every test. I will push an update that forces this, but by default everything should run with a single core for the tests.

glichtenstein commented 7 years ago

@chadlaing you are right, I forgotten about that, at some point I changed it to 8 in the t/output.t and I corrected as per suggestion. But it still fails every time in my server, I can't diagnose what's wrong with my setup, I've tried everything again from the beginning. Are my dependencies wrong?

I am using:

MUMmer3.23 perl (v5.22.1) CD-HIT version 4.7 (built on Jul 26 2017) muscle3.8.31_i86linux64 ncbi-blast-2.2.29+ and Ubuntu 16.04.2 LTS xenial

These are the steps I followed:

1)

glichtenstein@impam2:~$ git clone https://github.com/chadlaing/Panseq.git
Cloning into 'Panseq'...
remote: Counting objects: 4618, done.
remote: Total 4618 (delta 0), reused 0 (delta 0), pack-reused 4618
Receiving objects: 100% (4618/4618), 17.03 MiB | 1.74 MiB/s, done.
Resolving deltas: 100% (2542/2542), done.
Checking connectivity... done.

2)

glichtenstein@impam2:~$ cd Panseq/
glichtenstein@impam2:~/Panseq$ perl Build.PL
WARNING: the following files are missing in your kit:
    .idea/.name
    .idea/compiler.xml
    .idea/copyright/profiles_settings.xml
    .idea/encodings.xml
    .idea/inspectionProfiles/Project_Default.xml
    .idea/jscsPlugin.xml
    .idea/jsLinters/jscs.xml
    .idea/jsLinters/jshint.xml
    .idea/jsLinters/jslint.xml
    .idea/misc.xml
    .idea/modules.xml
    .idea/perl5local.xml
    .idea/vcs.xml
    .idea/workspace.xml
    _Inline/.lock
    _Inline/config-x86_64-linux-gnu-thread-multi-5.024001
    _Inline/lib/auto/Bio/DB/IndexedBase_168b/IndexedBase_168b.inl
    _Inline/lib/auto/Bio/DB/IndexedBase_168b/IndexedBase_168b.so
    lib/Interface/html/output/FriFeb2416182920175586.html
    lib/Interface/html/output/FriFeb2416182920175586.html.zip
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    lib/Interface/index.html
    lib/Interface/scripts/assembly_summary.txt
    lib/Interface/scripts/server.conf
    panseq.batch
    Panseq.iml
    t/plasmids.batch
    t/plasmids/accessoryGenomeFragments.fasta
    t/plasmids/binary.phylip
    t/plasmids/binary_table.txt
    t/plasmids/cdhit.fasta.clstr
    t/plasmids/core_snps.txt
    t/plasmids/coreGenomeFragments.fasta
    t/plasmids/locus_alleles.fasta
    t/plasmids/Master.log
    t/plasmids/pan_genome.txt
    t/plasmids/panGenome.fasta
    t/plasmids/panseq_results.zip
    t/plasmids/phylip_name_conversion.txt
    t/plasmids/snp.phylip
    t/plasmids/snp_table.txt
    t/query.batch
    t/query/accessoryGenomeFragments.fasta
    t/query/binary.phylip
    t/query/binary_table.txt
    t/query/core_snps.txt
    t/query/coreGenomeFragments.fasta
    t/query/locus_alleles.fasta
    t/query/Master.log
    t/query/pan_genome.txt
    t/query/panseq_results.zip
    t/query/phylip_name_conversion.txt
    t/query/snp.phylip
    t/query/snp_table.txt
Please inform the author.

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Panseq' version '3.1.1'

3)

glichtenstein@impam2:~/Panseq$ ./Build installdeps
All prerequisites satisfied

4)

glichtenstein@impam2:~/Panseq$ perl t/output.t --blastDirectory '/share/apps/ncbi-blast-2.2.29+/bin/' --mummerDirectory '/share/apps/MUMmer/' --cdhitDirectory '/share/apps/cdhit/' --muscleExecutable '/share/apps/muscle/muscle3.8.31_i86linux64' --type plasmids --removeRun 0 > testoutput_from_home_install.txt

# Failed test 'sha1CoreSnps generated correctly'
# at t/output.t line 221.
# +--------------------------------+----+--------------------------------+
# | GOT                            | OP | CHECK                          |
# +--------------------------------+----+--------------------------------+
# | 4c34b6ea16f000281413a51e7f1a96 | eq | 943a1cf71152037cb1543b0cacec2f |
# | cc                             |    | ff                             |
# +--------------------------------+----+--------------------------------+
# Failed test 'sha1PanGenome generated correctly'
# at t/output.t line 222.
# +--------------------------------+----+--------------------------------+
# | GOT                            | OP | CHECK                          |
# +--------------------------------+----+--------------------------------+
# | a5c4a6fefc6977063c136e0126a6e2 | eq | 6674c78f04dcbe10b569e247990e27 |
# | c9                             |    | b5                             |
# +--------------------------------+----+--------------------------------+
# Failed test 'sha1BinaryTable generated correctly'
# at t/output.t line 223.
# +--------------------------------+----+--------------------------------+
# | GOT                            | OP | CHECK                          |
# +--------------------------------+----+--------------------------------+
# | facdac694c0f7f8603f74151cdefd7 | eq | 9524c956d024e323de747623b67871 |
# | a6                             |    | e1                             |
# +--------------------------------+----+--------------------------------+
# Failed test 'sha1SnpTable generated correctly'
# at t/output.t line 224.
# +--------------------------------+----+--------------------------------+
# | GOT                            | OP | CHECK                          |
# +--------------------------------+----+--------------------------------+
# | 92a15888a3beee351cebc433024578 | eq | 883396f6d5f8d5d5918777a0a4ee6e |
# | 24                             |    | 97                             |
# +--------------------------------+----+--------------------------------+
# Failed test 'sha1SnpPhylip generated correctly'
# at t/output.t line 225.
# +--------------------------------+----+--------------------------------+
# | GOT                            | OP | CHECK                          |
# +--------------------------------+----+--------------------------------+
# | d490e061720aa36303cb3acbf55b4b | eq | 2ca6ba039d01c1ca0cf4bae11bd07c |
# | b3                             |    | fc                             |
# +--------------------------------+----+--------------------------------+
# Failed test 'sha1BinaryPhylip generated correctly'
# at t/output.t line 226.
# +--------------------------------+----+--------------------------------+
# | GOT                            | OP | CHECK                          |
# +--------------------------------+----+--------------------------------+
# | fd0779e2c1cacef90fbf5594a52cf8 | eq | 210104cefd498b805d040ae789e81f |
# | a6                             |    | 52                             |
# +--------------------------------+----+--------------------------------+
# Failed test 'sha1AccessoryFragments generated correctly'
# at t/output.t line 233.
# +--------------------------------+----+--------------------------------+
# | GOT                            | OP | CHECK                          |
# +--------------------------------+----+--------------------------------+
# | 399c70234d36995e76602614942550 | eq | 203f613ce413cc2e97f15134ae3fe6 |
# | 98                             |    | 27                             |
# +--------------------------------+----+--------------------------------+
# Failed test 'sha1CoreFragments generated correctly'
# at t/output.t line 234.
# +--------------------------------+----+--------------------------------+
# | GOT                            | OP | CHECK                          |
# +--------------------------------+----+--------------------------------+
# | a277c0f894016404a5570adb5236c3 | eq | bd5e19b696e6ef5602c3456e2792b4 |
# | 5f                             |    | 93                             |
# +--------------------------------+----+--------------------------------+
# Did not follow plan: expected 35, ran 26.

attached here is: testoutput_from_home_install.txt testoutput_from_home_install.txt

Thanks Chad,

BRGDS,

G.

chadlaing commented 7 years ago

Hi,

Can you pull the latest version of master and see if the tests pass? Everything on my end passes with blast+2.2.29; it is only the SHA1 tests that are failing on your end. Can you ensure that the Perl module Digest::SHA is installed?

Thanks, Chad

glichtenstein commented 7 years ago

Yes, it worked!!! I reinstalled SHA sudo cpan -I Digest::SHA and then sudo git pull and:

glichtenstein@impam2:/share/apps/Panseq$ more test_by_gabyl.sh 
perl t/output.t \
--blastDirectory '/share/apps/ncbi-blast-2.2.29+/bin/' \
--mummerDirectory '/share/apps/MUMmer/' \
--cdhitDirectory '/share/apps/cdhit/' \
--muscleExecutable '/share/apps/muscle/muscle3.8.31_i86linux64'
glichtenstein@impam2:/share/apps/Panseq$ bash test_by_gabyl.sh 
# Seeded srand with seed '20170809' from local date.
1..35
SCRIPT_LOCATION: t
Systemline: perl t/../lib/panseq.pl t/plasmids.batch
Loading setting allelesToKeep with value 2
Loading setting overwrite with value 1
Loading setting percentIdentityCutoff with value 90
Loading setting baseDirectory with value t/plasmids/
Loading setting muscleExecutable with value /share/apps/muscle/muscle3.8.31_i86linux64
Loading setting mummerDirectory with value /share/apps/MUMmer/
Loading setting cdhitDirectory with value /share/apps/cdhit/
Loading setting storeAlleles with value 1
Loading setting nameOrId with value name
Loading setting minimumNovelRegionSize with value 500
Loading setting blastDirectory with value /share/apps/ncbi-blast-2.2.29+/bin/
Loading setting queryDirectory with value t/data/plasmids/
Loading setting coreGenomeThreshold with value 2
Loading setting numberOfCores with value 1
Loading setting cdhit with value 1
Loading setting fragmentationSize with value 500
Loading setting runMode with value pan
Settings file: t/plasmids.batch

The directory you have specified for program output:
    t/plasmids/
already exists.
overwrite: 1
Overwrite set to true. Deleting directory t/plasmids/
2017/08/09 12:12:13 INFO |  NovelIterator.pm:186> We have 5 genomes this run 
2017/08/09 12:12:18 INFO |  Panseq.pm:268> Panseq mode set as pan 
2017/08/09 12:12:18 INFO |  SegmentMaker.pm:164> Segmenting t/plasmids/83cebb2c6208952b05599fd6693a5813_26f912cf187ef5c0e270e34f6bf2044a into 500bp segments 
2017/08/09 12:12:18 INFO |  Panseq.pm:310> Running cd-hit with:
/share/apps/cdhit/cd-hit-est -M 0 -T 1 -c 0.9 -s 0.9 -i t/plasmids/pangenome_fragments.fasta -o t/plasmids/cdhit.fasta 
================================================================
Program: CD-HIT, V4.7 (+OpenMP), Jul 26 2017, 15:16:41
Command: /share/apps/cdhit/cd-hit-est -M 0 -T 1 -c 0.9 -s 0.9
         -i t/plasmids/pangenome_fragments.fasta -o
         t/plasmids/cdhit.fasta

Started: Wed Aug  9 12:12:18 2017
================================================================
                            Output                              
----------------------------------------------------------------
total seq: 481
longest and shortest : 957 and 500
Total letters: 244190
Sequences have been sorted

Approximated minimal memory consumption:
Sequence        : 0M
Buffer          : 1 X 12M = 12M
Table           : 1 X 16M = 16M
Miscellaneous   : 4M
Total           : 33M

Table limit with the given memory limit:
Max number of representatives: 4000000
Max number of word counting entries: 300478500

comparing sequences from          0  to        481

      481  finished        481  clusters

Apprixmated maximum memory consumption: 35M
writing new database
writing clustering information
program completed !

Total CPU time 0.48
2017/08/09 12:12:19 INFO |  FastaFileSplitter.pm:127> Splitting t/plasmids/cdhit.fasta into 1 files 
2017/08/09 12:12:20 INFO |  PanGenome.pm:210> Analyzing the pan-genome 
2017/08/09 12:12:20 INFO |  PanGenome.pm:215> Processing Blast output files 
2017/08/09 12:12:24 INFO |  PanGenome.pm:543> Total results: 481 
2017/08/09 12:12:25 INFO |  PanGenome.pm:303> Processing blast output files complete 
2017/08/09 12:12:25 INFO |  PanGenome.pm:304> Pan-genome generation complete 
2017/08/09 12:12:25 INFO |  Panseq.pm:524> Creating zip file 
Systemline: perl t/../lib/panseq.pl t/query.batch
Loading setting queryDirectory with value t/data/genomes/
Loading setting coreGenomeThreshold with value 2
Loading setting blastDirectory with value /share/apps/ncbi-blast-2.2.29+/bin/
Loading setting minimumNovelRegionSize with value 1
Loading setting nameOrId with value name
Loading setting storeAlleles with value 1
Loading setting queryFile with value t/data/testfragments.fasta
Loading setting runMode with value pan
Loading setting fragmentationSize with value 0
Loading setting numberOfCores with value 1
Loading setting percentIdentityCutoff with value 90
Loading setting overwrite with value 1
Loading setting mummerDirectory with value /share/apps/MUMmer/
Loading setting muscleExecutable with value /share/apps/muscle/muscle3.8.31_i86linux64
Loading setting baseDirectory with value t/query/
Settings file: t/query.batch

The directory you have specified for program output:
    t/query/
already exists.
overwrite: 1
Overwrite set to true. Deleting directory t/query/
2017/08/09 12:12:26 INFO |  Panseq.pm:268> Panseq mode set as pan 
2017/08/09 12:12:26 INFO |  FastaFileSplitter.pm:127> Splitting t/query/sanitized_queryFile.fasta into 1 files 
2017/08/09 12:12:27 INFO |  PanGenome.pm:210> Analyzing the pan-genome 
2017/08/09 12:12:27 INFO |  PanGenome.pm:215> Processing Blast output files 
2017/08/09 12:12:27 INFO |  PanGenome.pm:543> Total results: 10 
2017/08/09 12:12:28 WARN |  CombineFilesIntoSingleFile.pm:83> Skipping t/query/1_accessoryGenomeFragments as it has size of 0 
2017/08/09 12:12:28 INFO |  PanGenome.pm:303> Processing blast output files complete 
2017/08/09 12:12:28 INFO |  PanGenome.pm:304> Pan-genome generation complete 
2017/08/09 12:12:28 INFO |  Panseq.pm:524> Creating zip file 
Systemline: perl t/../lib/panseq.pl t/genomes.batch
Loading setting baseDirectory with value t/genomes/
Loading setting mummerDirectory with value /share/apps/MUMmer/
Loading setting muscleExecutable with value /share/apps/muscle/muscle3.8.31_i86linux64
Loading setting percentIdentityCutoff with value 90
Loading setting overwrite with value 1
Loading setting numberOfCores with value 1
Loading setting runMode with value pan
Loading setting fragmentationSize with value 1000
Loading setting queryDirectory with value t/data/genomes/
Loading setting coreGenomeThreshold with value 3
Loading setting blastDirectory with value /share/apps/ncbi-blast-2.2.29+/bin/
Loading setting minimumNovelRegionSize with value 1000
Loading setting nameOrId with value name
Settings file: t/genomes.batch
2017/08/09 12:12:28 INFO |  NovelIterator.pm:186> We have 6 genomes this run 
2017/08/09 12:13:02 INFO |  Panseq.pm:268> Panseq mode set as pan 
2017/08/09 12:13:02 INFO |  SegmentMaker.pm:164> Segmenting t/genomes/edfc6cac3fd4427a802625d82d978a4e_055fa1515be783d915e9dd57167d00f2 into 1000bp segments 
2017/08/09 12:13:03 INFO |  FastaFileSplitter.pm:127> Splitting t/genomes/pangenome_fragments.fasta into 1 files 
2017/08/09 12:13:20 INFO |  PanGenome.pm:210> Analyzing the pan-genome 
2017/08/09 12:13:20 INFO |  PanGenome.pm:215> Processing Blast output files 
2017/08/09 12:16:49 INFO |  PanGenome.pm:543> Total results: 6002 
2017/08/09 12:16:50 WARN |  CombineFilesIntoSingleFile.pm:83> Skipping t/genomes/1_locus_alleles as it has size of 0 
2017/08/09 12:16:50 INFO |  PanGenome.pm:303> Processing blast output files complete 
2017/08/09 12:16:50 INFO |  PanGenome.pm:304> Pan-genome generation complete 
2017/08/09 12:16:50 INFO |  Panseq.pm:524> Creating zip file 
Systemline: perl t/../lib/panseq.pl t/sha1.batch
Loading setting fragmentationSize with value 500
Loading setting sha1 with value 1
Loading setting runMode with value pan
Loading setting numberOfCores with value 1
Loading setting nameOrId with value name
Loading setting minimumNovelRegionSize with value 500
Loading setting blastDirectory with value /share/apps/ncbi-blast-2.2.29+/bin/
Loading setting queryDirectory with value t/data/plasmids/
Loading setting coreGenomeThreshold with value 2
Loading setting storeAlleles with value 1
Loading setting muscleExecutable with value /share/apps/muscle/muscle3.8.31_i86linux64
Loading setting mummerDirectory with value /share/apps/MUMmer/
Loading setting baseDirectory with value t/sha1/
Loading setting allelesToKeep with value 2
Loading setting overwrite with value 1
Loading setting percentIdentityCutoff with value 90
Settings file: t/sha1.batch

The directory you have specified for program output:
    t/sha1/
already exists.
overwrite: 1
Overwrite set to true. Deleting directory t/sha1/
2017/08/09 12:16:53 INFO |  NovelIterator.pm:186> We have 5 genomes this run 
2017/08/09 12:16:57 INFO |  Panseq.pm:268> Panseq mode set as pan 
2017/08/09 12:16:57 INFO |  SegmentMaker.pm:164> Segmenting t/sha1/322ce628f4205db149fe2c1599e7e6d1_b883afe64ed288dec54afe2c1657569c into 500bp segments 
2017/08/09 12:16:57 INFO |  FastaFileSplitter.pm:127> Splitting t/sha1/pangenome_fragments.fasta into 1 files 
2017/08/09 12:16:58 INFO |  PanGenome.pm:210> Analyzing the pan-genome 
2017/08/09 12:16:58 INFO |  PanGenome.pm:215> Processing Blast output files 
2017/08/09 12:17:02 INFO |  PanGenome.pm:543> Total results: 481 
2017/08/09 12:17:03 INFO |  PanGenome.pm:303> Processing blast output files complete 
2017/08/09 12:17:03 INFO |  PanGenome.pm:304> Pan-genome generation complete 
2017/08/09 12:17:03 INFO |  Panseq.pm:524> Creating zip file 
ok 1 - plasmidsCoreSnps generated correctly
ok 2 - plasmidsPanGenome generated correctly
ok 3 - plasmidsBinaryTable generated correctly
ok 4 - plasmidsSnpTable generated correctly
ok 5 - plasmidsSnpPhylip generated correctly
ok 6 - plasmidsBinaryPhylip generated correctly
ok 7 - plasmidsNameConversion generated correctly
ok 8 - plasmidsAccessoryFragments generated correctly
ok 9 - plasmidsCoreFragments generated correctly
ok 10 - queryCoreSnps generated correctly
ok 11 - queryPanGenome generated correctly
ok 12 - queryBinaryTable generated correctly
ok 13 - querySnpTable generated correctly
ok 14 - querySnpPhylip generated correctly
ok 15 - queryBinaryPhylip generated correctly
ok 16 - queryNameConversion generated correctly
ok 17 - queryAlleles generated correctly
ok 18 - genomesCoreSnps generated correctly
ok 19 - genomesPanGenome generated correctly
ok 20 - genomesBinaryTable generated correctly
ok 21 - genomesSnpTable generated correctly
ok 22 - genomesSnpPhylip generated correctly
ok 23 - genomesBinaryPhylip generated correctly
ok 24 - genomesNameConversion generated correctly
ok 25 - genomesAccessoryFragments generated correctly
ok 26 - genomesCoreFragments generated correctly
ok 27 - sha1CoreSnps generated correctly
ok 28 - sha1PanGenome generated correctly
ok 29 - sha1BinaryTable generated correctly
ok 30 - sha1SnpTable generated correctly
ok 31 - sha1SnpPhylip generated correctly
ok 32 - sha1BinaryPhylip generated correctly
ok 33 - sha1NameConversion generated correctly
ok 34 - sha1AccessoryFragments generated correctly
ok 35 - sha1CoreFragments generated correctly

Thank you 100:

chadlaing commented 7 years ago

Great!