Taxonomic Assignment error with latest version

Scott Handley

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Apr 4, 2016, 2:25:27 PM4/4/16

to LotuS rRNA pipeline

Hi!

Just thought I would let you know I am getting an error in the taxonomic assignment portion of the newest update (4 April, 2016). Here is a snippet of the error I get from the output.

Sample 16812 id Bacteria does not exist. Species. Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;Akkermansia;muciniphila;OTU_302.

Sample 16813 id Bacteria does not exist. Species. Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;Akkermansia;muciniphila;OTU_302.

Sample 16814 id Bacteria does not exist. Species. Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;Akkermansia;muciniphila;OTU_302.

Sample 16815 id Bacteria does not exist. Species. Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;Akkermansia;muciniphila;OTU_302.

Total reads in matrix: 0

TaxLvl %AssignedReads %AssignedTax

Illegal division by zero at ./lotus.pl line 1711.

I ran the exact same commands I do with the previous version. Let me know if you want to see a specific log file.

Scott Handley

Falk Hildebrand

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Apr 4, 2016, 2:41:15 PM4/4/16

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Hey Scott,

can you please send me the LotuS_runlog.txt file?

cheers,

Falk

Scott Handley

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Apr 4, 2016, 2:53:52 PM4/4/16

to LotuS rRNA pipeline

Google Drive link to file. It was too big to attach to the reply:

https://drive.google.com/file/d/0B_pMICKIYsdaS05QNzAxc2F6TXM/view?usp=sharing

Falk Hildebrand

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Apr 4, 2016, 2:59:34 PM4/4/16

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Seems like the LCA C++ program did not start correctly. Can you check if you have a file called "./LCA" in your dir? Is there a LCA_src folder*? O/w please reinstall from the lotus webpage. Sorry about this, but the update via autoinstall.pl on the weekend didn't have the correct links set for the LCA_src files.

* (there you could try to compile manually, copy to the lotus dir and check that the lotus.cfg contains a line "LCA ./LCA")

I will also try to reproduce your error in the next days.

best,

Falk

Scott Handley

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Apr 4, 2016, 4:53:35 PM4/4/16

to LotuS rRNA pipeline

Install from the web site fixed everything. You were correct. The LCA_src directory wasn't there. Just did a full run and got all the expected files.

Thanks Falk!

Scott

Falk Hildebrand

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Apr 4, 2016, 6:41:35 PM4/4/16

to LotuS rRNA pipeline

Great! I also updated the autoinstaller in the new lotus version, and the bug is fixed with the Legacy Perl LCA implementation!

best,
Falk

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