search

oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
315 stars 70 forks source link

Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184. #438

Closed CongyangY closed 3 months ago

CongyangY commented 3 months ago

Hi, when I use the EDTA.pl to annotate the plant genome, I found the run log print many similar errors like this:

Sun Feb 25 12:13:23 CST 2024    Perform EDTA advance filtering for raw TE candidates and generate the stage 1 library:

Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $len in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $len in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $len in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $len in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $len in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $len in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.
Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184.

And the step has been running about four days,I don't know if it is correct, and if I should do some fixes to avoid the output of this error message?

CongyangY commented 3 months ago

I also use the EDTA program to annotate the another plants(B), with similar lineage compare with the above plants(A). I selected the 200Mb size of B plants to annotate, and it spend about two days to finish annotate. There is no error information like the above issues in the annotation step.

oushujun commented 3 months ago

Sorry for the delay. Seems to me they are random errors and should not impact your results. Please let me know if you have more questions. Thanks!

Shujun