rob-p
commented
8 years ago Hi Chris,
When you say "previous" version, do you mean v0.6.3? One thing that has changed (and I will update the documentation to make this more clean) is that the k value you provide to the indexer must be an odd value. That means, you can't say e.g. -k 18 or -k 20. Rather, -k 19 or -k 21 should work. It should complain if you give an even value, so I'll double-check that it does that.
--Rob
P.S. You can actually run the indexer now without a -k argument, and it will assume a default value.
butterflyology
Just installed Sailfish 0.7.5 from the previous version (which worked fine).
Installed the new version, rebuilt the index for my experiment, and now I get:
"[2015-10-05 14:39:23.044] [jointLog] [info] parsing read library format there is 1 lib Exception : [Error: The index version file Sail-0.3-index/versionInfo.json doesn't seem to exist. Please try re-building the salmon index.] /home/chamm/Sailfish/bin/sailfish quant was invoked improperly. For usage information, try /home/chamm/Sailfish/bin/sailfish quant --help Exiting."
I try rebuilding the index, including using --force and just deleting the directory with the index, and I still get this error. When I build the new index, it seems to have far less output then before. I hope this helps.
Chris