error exit

[Jianz9293]

X_nanoraw.txt

Dear author, I encountered an error when running the software, exit 120 is displayed. Could you please help me check the reason? I have attached the command line and log below, thank you very much

command: Exit 120 nohup TEsorter /gpfs1/home/life/dengcl/Sp_TUseq/X_assemblegenome1.fa -db rexdb-plant -p 20 -cov 20 -eval 1e-3 > X_nanoraw.file 2>&1 (wd: ~/zhoujian/TEsorter/Xnanoraw)

[zhangrengang]

The log seems to be not completely showed at the end:

Traceback (most recent call last):

Did any other information print after this line?

[Jianz9293]

There is nothing under this line，What might be the problem?

[zhangrengang]

It is abnormal for python Traceback and I have no sense about what is wrong. Please try with the test data and let me known what errors raise.

[zhangrengang]

Which version are you using, the conda version or the last github version?

[zhangrengang]

A normal python traceback is like this:

     Traceback(most recent call last):
     File"main.py", line108, in < module >
     lumberjack()
     File"main.py", line102, in lumberjack
     bright_side_of_death()
     File"/main.py", line105, in bright_side_of_death
     return print(tuple()[0])
     IndexError: tuple index out of range

which will indicate where and which error raise.

[Jianz9293]

text.txt Thank you for your reply. Conda version is 4.11.0. I just ran text, and the log is as follows. Looks like it's working

[Jianz9293]

I did see this kind of error in the log of another running program. The other program reported the following error messages Y_nanoraw.txt File.txt TEsorter.txt

[zhangrengang]

The traceback also seems to be incomplete:

2022-03-01 20:34:26,784 -INFO- classifying the unclassified sequences by searching against the classified ones
Traceback (most recent call last):
  File "/gpfs1/home/life/dengcl/anaconda3/lib/python3.9/site-packages/Bio/File.py", line 72, in as_handle
    with open(handleish, mode, **kwargs) as fp:
TypeError: expected str, bytes or os.PathLike object, not TextIOWrapper

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs1/home/life/dengcl/anaconda3/bin/TEsorter", line 10, in <module>
    sys.exit(main())

Could you send me a subset of your data to me to test?

[Jianz9293]

The size of my data is about 15G, how should I send it to you?If I send only part of the data, I don't know if the result is accurate.

[zhangrengang]

You can extract a part of the data and test whether the issue is reproducible. If so, just send me the partial data via email (zhangrengang@ori-gene.cn) or Baidu Cloud (YunPan).

[oushujun]

Judging from the input file name they may have provided the entire genome to TEsorter?

Shujun

On Wed, Mar 2, 2022 at 5:36 AM zhangrengang @.***> wrote:

You can extract a part of the data and test whether the issue is reproducible. If so, just send me the partial data via email ( @.***) or Baidu Cloud (YunPan).

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