JCVI-Cloud/CloudVIGOR — Issue #1: Validation tests failing on Eucalyptus
Author: tprindle
Created: 2011-12-22 17:16:29+00:00
State: open

1. I had to comment out the first test because there is a path in the
related configuration file which is JCVI specific, so I'll have to work
with Jeff on that. This causes the missing files in the diff.
2. For some reason, clustalw does not appear to be executing. This is causing the output to be different, although it may not be the only issue.

Error Output:
```[172.17.31.103] run: diff -qr /usr/local/scratch/vigor-scratch/validate-test-data /usr/local/scratch/vigor-scratch/test-output
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.aln
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.cds
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.fs
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.pep
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.stats
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.tbl
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/FluB.aln and /usr/local/scratch/vigor-scratch/test-output/FluB.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/FluB.cds and /usr/local/scratch/vigor-scratch/test-output/FluB.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/FluB.pep and /usr/local/scratch/vigor-scratch/test-output/FluB.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/FluB.stats and /usr/local/scratch/vigor-scratch/test-output/FluB.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/FluB.tbl and /usr/local/scratch/vigor-scratch/test-output/FluB.tbl differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32265.aln and /usr/local/scratch/vigor-scratch/test-output/GCV_32265.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32265.cds and /usr/local/scratch/vigor-scratch/test-output/GCV_32265.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32265.pep and /usr/local/scratch/vigor-scratch/test-output/GCV_32265.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32265.stats and /usr/local/scratch/vigor-scratch/test-output/GCV_32265.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32265.tbl and /usr/local/scratch/vigor-scratch/test-output/GCV_32265.tbl differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.aln and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.cds and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.fs and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.fs differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.pep and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.stats and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.tbl and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.tbl differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_35931.aln and /usr/local/scratch/vigor-scratch/test-output/GCV_35931.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_35931.cds and /usr/local/scratch/vigor-scratch/test-output/GCV_35931.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_35931.pep and /usr/local/scratch/vigor-scratch/test-output/GCV_35931.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_35931.stats and /usr/local/scratch/vigor-scratch/test-output/GCV_35931.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_35931.tbl and /usr/local/scratch/vigor-scratch/test-output/GCV_35931.tbl differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/Rhinovirus_genomes.aln and /usr/local/scratch/vigor-scratch/test-output/Rhinovirus_genomes.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/Rhinovirus_genomes.cds and /usr/local/scratch/vigor-scratch/test-output/Rhinovirus_genomes.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/Rhinovirus_genomes.pep and /usr/local/scratch/vigor-scratch/test-output/Rhinovirus_genomes.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/Rhinovirus_genomes.stats and /usr/local/scratch/vigor-scratch/test-output/Rhinovirus_genomes.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/Rhinovirus_genomes.tbl and /usr/local/scratch/vigor-scratch/test-output/Rhinovirus_genomes.tbl differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/rotaV_10_22_genome.aln and /usr/local/scratch/vigor-scratch/test-output/rotaV_10_22_genome.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/rotaV_10_22_genome.cds and /usr/local/scratch/vigor-scratch/test-output/rotaV_10_22_genome.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/rotaV_10_22_genome.pep and /usr/local/scratch/vigor-scratch/test-output/rotaV_10_22_genome.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/rotaV_10_22_genome.stats and /usr/local/scratch/vigor-scratch/test-output/rotaV_10_22_genome.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/rotaV_10_22_genome.tbl and /usr/local/scratch/vigor-scratch/test-output/rotaV_10_22_genome.tbl differ
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: vigor-test-output.tgz
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/YFV_genome.aln and /usr/local/scratch/vigor-scratch/test-output/YFV_genome.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/YFV_genome.cds and /usr/local/scratch/vigor-scratch/test-output/YFV_genome.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/YFV_genome.pep and /usr/local/scratch/vigor-scratch/test-output/YFV_genome.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/YFV_genome.stats and /usr/local/scratch/vigor-scratch/test-output/YFV_genome.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/YFV_genome.tbl and /usr/local/scratch/vigor-scratch/test-output/YFV_genome.tbl differ
[172.17.31.103] out:

Fatal error: run() encountered an error (return code 1) while executing 'diff -qr /usr/local/scratch/vigor-scratch/validate-test-data /usr/local/scratch/vigor-scratch/test-output'

Aborting.
```