PanSeq Core and Pan SNPs

[Moorem]

Hi guys,

I've had some issues running PanSeq, has anyone else come across this? There is absolutely no problem with my input files and when I run the test (t/output.t) it fails also.

Thanks in advance for any help!

[TiborNagy]

If t/output.t fails, it means you installation is not correct. What kind of error messages do you get?

[Moorem]

Thanks so much for replying! Firstly all of the pre-requisites are installed and it confirms this when build was successful, so there is no issue there with the installation. I have also re-downloaded the entire thing and re-installed it to get the exact same issues and the issues are the same whether or not I change my file paths in t/output.t to the correct blast+ and mummer directories and muscle executable.

The output returns no 'FATAL' values, seems to run through fine but at the end returns errors. When I run with my query files it runs for a few lines and then stops.

This is the output.t, output which I refer to:

The directory you have specified for program output:
./genomes/
already exists. Please specify a new baseDirectory
✖ plasmidsCoreSnps generated correctly
# Failed test 'plasmidsCoreSnps generated correctly'
# at output.t line 126.
# got: 'f34624e6e3b1eca098804c4f2423058a'
# expected: 'db76a69bf6a6de4c8a4892eeb3efc444'
✖ plasmidsPanGenome generated correctly
# Failed test 'plasmidsPanGenome generated correctly'
# at output.t line 127.
# got: 'bd7a787a04e3c453dbbd8ef10664a7ac'
# expected: '520e12c7b588dea7dbf68aee14c81066'
✖ plasmidsBinaryTable generated correctly
# Failed test 'plasmidsBinaryTable generated correctly'
# at output.t line 128.
# got: '7ee21a7550e9bf55d78c9c747b2f5ae8'
# expected: '16d5468e64301223914321185ad8e845'
✖ plasmidsSnpTable generated correctly
# Failed test 'plasmidsSnpTable generated correctly'
# at output.t line 129.
# got: 'bd81ad5f4d43dd1e2362668885622791'
# expected: '3b85b92e0e930741f360bc18668d2378'
✖ plasmidsSnpPhylip generated correctly
# Failed test 'plasmidsSnpPhylip generated correctly'
# at output.t line 130.
# got: '03a39ae42545fff9b7a4371fdcef4d48'
# expected: '2eb68d2fdcb140599210116cb96c4c8d'
✖ plasmidsBinaryPhylip generated correctly
# Failed test 'plasmidsBinaryPhylip generated correctly'
# at output.t line 131.
# got: 'a0605c1bc9adafa676240563d34a7077'
# expected: 'ec3d516ca77e84639f01bd31c83a0983'
✓ queryCoreSnps generated correctly
✓ queryPanGenome generated correctly
✓ queryBinaryTable generated correctly
✓ querySnpTable generated correctly
✓ querySnpPhylip generated correctly
✓ queryBinaryPhylip generated correctly
✓ queryAlleles generated correctly
✖ genomesCoreSnps generated correctly
# Failed test 'genomesCoreSnps generated correctly'
# at output.t line 126.
# got: undef
# expected: '5ccf9a59c9324607ae2bc4b859a2c216'
✖ genomesPanGenome generated correctly
# Failed test 'genomesPanGenome generated correctly'
# at output.t line 127.
# got: undef
# expected: '44619ab2f10d75509b8a8993cb900223'
✖ genomesBinaryTable generated correctly
# Failed test 'genomesBinaryTable generated correctly'
# at output.t line 128.
# got: undef
# expected: 'dd6723f30271de76053935b3adcbc62f'
✖ genomesSnpTable generated correctly
# Failed test 'genomesSnpTable generated correctly'
# at output.t line 129.
# got: undef
# expected: '454837ace243d559171273f35b0352f0'
✖ genomesSnpPhylip generated correctly
# Failed test 'genomesSnpPhylip generated correctly'
# at output.t line 130.
# got: undef
# expected: '38e50cb985fee5f4bee23ea240dd7758'
✖ genomesBinaryPhylip generated correctly
# Failed test 'genomesBinaryPhylip generated correctly'
# at output.t line 131.
# got: undef
# expected: 'f73de672af16e1d1c654b1b6abdac9ff'





Thanks in advance if you can help with this!!