Worry about warning and determine if they are errors

[byeollee]

Hi,

I am writing to enquire about Corason.

When analyzing CORASON with docker, I see the following statement.

Use of uninitialized value $hit in string eq at /opt/corason/CORASON/1_Context_text.pl line 272.

--------------------- WARNING ---------------------
MSG: Can not set Bio::Location::Simple::end() equal to start; start not set

I want to know if this is an error, and if so, how can I fix it?

I type the command as follows

~/run_corason "fasta file location" "gbks file location" "query gbk file location" -g

Thanks.

[nselem]

Hello
I'm sorry for not getting back to you sooner. Its just a warning, it should have worked. Were you able to run corason?

[Mohsin0911]

if someone is looking this , please help me am also getting same issues, [email protected]:

Sequences didnt align, I will draw SVG clusters with the single hits blast order
grep: /home/output/yourquery.query-output//home/output/yourquery.query-output.BLAST: No such file or directory
grep: /home/output/yourquery.query-output//home/output/yourquery.query-output.BLAST: No such file or directory
grep: /home/output/yourquery.query-output//home/output/yourquery.query-output.BLAST: No such file or directory
grep: /home/output/yourquery.query-output//home/output/yourquery.query-output.BLAST: No such file or directory
grep: /home/output/yourquery.query-output//home/output/yourquery.query-output.BLAST: No such file or directory
grep: /home/output/yourquery.query-output//home/output/yourquery.query-output.BLAST: No such file or directory
grep: /home/output/yourquery.query-output//home/output/yourquery.query-output.BLAST: No such file or directory
grep: /home/output/yourquery.query-output//home/output/yourquery.query-output.BLAST: No such file or directory
grep: /home/output/yourquery.query-output//home/output/yourquery.query-output.BLAST: No such file or directory
Use of uninitialized value $INPUTS in scalar chop at /opt/corason/CORASON/CoreCluster.pl line 281.

Draw
Use of uninitialized value $INPUTS in concatenation (.) or string at /opt/corason/CORASON/CoreCluster.pl line 230.
Now SVG file will be generated with inputs:

Use of uninitialized value $INPUTS in concatenation (.) or string at /opt/corason/CORASON/CoreCluster.pl line 231.
Use of uninitialized value $INPUTS in concatenation (.) or string at /opt/corason/CORASON/CoreCluster.pl line 232.
/opt/corason/CORASON/3_Draw.pl 85000 /home/output/yourquery.query-output yourquery.querycouldn open frequency file yourquery.query/Frequency Not a directory
at /opt/corason/CORASON/3_Draw.pl line 113.
SVG file generated

mv: cannot stat '/home/output/yourquery.query-output/Contextos.svg': No such file or directory
Cleaning temporary files
rm: cannot remove '/home/output/yourquery.query-output/PrincipalHits.muscle-gb.htm': No such file or directory
rm: cannot remove '/home/output/yourquery.query-output/*.txt': No such file or directory
rm: cannot remove '/home/output/yourquery.query-output/CORASON_GENOMES': No such file or directory
mv yourquery.query /home/output/Done
Have a nice day

[nselem]

Hello, sorry for the long delay. You can write an email [email protected], we can set a zoom call and try to solve it.