Use of unitialized value $chr_pre in has element call_seq_by_list.pl line 87

[sjteresi]

Hello Shujun,

I was running EDTA v2.0.0 on a small cranberry genome and got the following error: Use of uninitialized value $chr_pre in hash element at /mnt/home/teresisc/anaconda3/envs/EDTA/share/LTR_retriever/bin/call_seq_by_list.pl line 87.

The pipeline does not fail and continues to run. I looked for similar issues in your repo and only ever found this error occurring in the context of something else (usually it seemed like this error was a by-product of some bigger error). The small genome check works just fine and so does the dependency check. I also would like to note that this has not occurred for the other 3 cranberry genomes I am running, and has not occurred for 8 other blueberry genomes that are running.

Is this something I should be concerned about, or should I just let it ride? I can provide you with my input files if desired.

Thank you very much for your time and consideration!

Sincerely, Scott Teresi

[oushujun]

Hi Scott,

You may Check the pass.list file in the raw/LTR folder. If the line count is similar to those of other cranberry genomes, that should be fine. I will further look into the code and see if there's any big issues.

Shujun

On Thu, Mar 31, 2022 at 12:29 PM Scott Teresi @.***> wrote:

Hello Shujun,

I was running EDTA v2.0.0 on a small cranberry genome and got the following error: Use of uninitialized value $chr_pre in hash element at /mnt/home/teresisc/anaconda3/envs/EDTA/share/LTR_retriever/bin/ call_seq_by_list.pl line 87.

The pipeline does not fail and continues to run. I looked for similar issues in your repo and only ever found this error occurring in the context of something else (usually it seemed like this error was a by-product of some bigger error). The small genome check works just fine and so does the dependency check. I also would like to note that this has not occurred for the other 3 cranberry genomes I am running, and has not occurred for 8 other blueberry genomes that are running.

Is this something I should be concerned about, or should I just let it ride? I can provide you with my input files if desired.

Thank you very much for your time and consideration!

Sincerely, Scott Teresi

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[sjteresi]

It does indeed seem to have a similar amount of lines. Each genome (only have 3 others available to compare with at the moment) had ~2100 lines in the pass.list file.

[oushujun]

Based on this information, it Maybe just a minor glitch.

On Thu, Mar 31, 2022 at 2:41 PM Scott Teresi @.***> wrote:

It does indeed seem to have a similar amount of lines. Each genome (only have 3 others available to compare with at the moment) had ~2100 lines in the pass.list file.

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