DESeq2 ascii codec can't encode character

Question: DESeq2 ascii codec can't encode character

2.8 years ago by

France

Hello everyone,

I have this error when I try to use DESeq2 1.8.2 from iuc team :

I guess there is a special character in one of the htseq-count output because the gff file contains it. I tried to clean the gff file to regenerate the htcount outputs, but I still have the same issue (but I could have "forget" one special character)

I would like to find the good place to make things work, like by adding something to decode/encode the string that create this error. First, I wonder if the issue comes from python, the DB (in postgresql which is in UTF8) or from R script. The error suggests that it is in python, but i'm not that sure about that.

Any guidance would be very appreciated, did you already met this error ?

Thank you !

Christ

ascii codec character deseq2 • 1.0k views

ADD COMMENT • link •

modified 2.7 years ago • written 2.8 years ago by christophe.habib • 340

It's more likely that the unicode character is included in the stderr or stdout. Can you check your locale setting of your Galaxy host and switch them to UTF-8 if possible.

ADD REPLY • link written 2.7 years ago by Bjoern Gruening ♦ 5.1k

I just switched all locales to fr_FR.UTF-8. And I restarted the galaxy instance.

LANG=fr_FR.UTF-8
LANGUAGE=
LC_CTYPE="fr_FR.UTF-8"
LC_NUMERIC="fr_FR.UTF-8"
LC_TIME="fr_FR.UTF-8"
LC_COLLATE="fr_FR.UTF-8"
LC_MONETARY="fr_FR.UTF-8"
LC_MESSAGES="fr_FR.UTF-8"
LC_PAPER="fr_FR.UTF-8"
LC_NAME="fr_FR.UTF-8"
LC_ADDRESS="fr_FR.UTF-8"
LC_TELEPHONE="fr_FR.UTF-8"
LC_MEASUREMENT="fr_FR.UTF-8"
LC_IDENTIFICATION="fr_FR.UTF-8"
LC_ALL=

But the issue is still here. Do I have to regenerate the htseq-count files before trying to use DESeq2 again ?

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by christophe.habib • 340

I tried to regenerate all htseq-count files, it still doesn't work..

I just noticed that my DB was actually in ASCII :

 server_encoding
-----------------
 SQL_ASCII

So I guess the issue is here. How do I change this properly ? I found that :

Dump your database
Drop your database,
Create new database with the different encoding
Reload your data.

Is that OK ? Do I have something else to do on the dumped database like managing the special charaters before reloading it ?

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by christophe.habib • 340

UPDATE pg_database SET datistemplate = FALSE WHERE datname = 'template1'; ALTER DATABASE template1 RENAME to templatebackup; CREATE DATABASE template1 WITH TEMPLATE = template0 ENCODING = 'UNICODE'; UPDATE pg_database SET datistemplate = TRUE WHERE datname = 'template1'; \c template1 VACUUM FREEZE;

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