searchp --output-columns option with taxonomy columns

[uludag]

I downloaded prebuild UniProt index using the link given on the pre-build indexes wiki page where Tax option is checked for the index.

If I add staxids or lcaid options to --output-columns specifier such as "std staxids", I get too-many-arguments error. Taxonomic-Workflows wiki page suggests combined column options should work. If I specify staxids or lcaid options alone I don't get any errors. --mahmut

[h-2]

I am currently on vacation and will have a look at this next week in detail. However, please check if single quotes work instead of double quotes, i.e. --output-columns 'std qacc'. Depending on your shell or your shell-script this might make a difference.

[uludag]

I have checked that single quotes, i.e. --output-columns 'std qacc' doesn't change the error message returned

[h-2]

Sorry for the late reply. I have tried to reproduce the issue, but everything works fine here.
Can you give me the following information:

• output of uname -a
• contents of /etc/debian_version if it exists
• output of $SHELL --version
• output of bin/lambda2 --version

Thanks and sorry again for the late reply.

[uludag]

I just have found that above error is limited to the lambda2 executable in lambda2-1.9.4-Linux-x86_64.tar.xz. It looks I don't get error if I use the lambda2 executable, version 1.9.4, compiled on my machine earlier

I don't have /etc/debian_version on my machine

I select/copied the outputs you asked here:

Linux 3.10.0-514.21.1.el7.x86_64 #1 SMP Thu May 25 17:04:51 UTC 2017
GNU bash, version 4.2.46(1)-release (x86_64-redhat-linux-gnu)
lambda2 version: 1.9.4
SeqAn version: 2.4.0

[h-2]

I can confirm the issue, it's due to some problem in the argument parser related to static builds, I will try to track it down next week!

[h-2]

Should be fixed in current master!

[h-2]

(it wasn't the argument parser after all, but the my shell script that dispatches to the binaries 🙈 )