LTR_FINDER_parallel running error

[LarsonWang]

Hello, I encountered this error when i was using LTR_FINDER_parallel:

$ perl LTR_FINDER_parallel -seq Chr.fasta -finder /home/csw3/anaconda3/envs/1/bin

Using this LTR_FINDER: /home/csw3/anaconda3/envs/1/bin/
Pass!
Tue Aug 15 07:23:53 2023 CPU1: running on ch_01_sub1
open ch_01_sub1 error!
Tue Aug 15 07:23:53 2023 CPU1: ch_01_sub1 timeout, process it with the salvage mode
Tue Aug 15 07:23:53 2023 CPU2: running on ch_01_sub2
open ch_01_sub2 error!
Tue Aug 15 07:23:53 2023 CPU2: ch_01_sub2 timeout, process it with the salvage mode
Tue Aug 15 07:23:53 2023 CPU3: running on ch_01_sub3
open ch_01_sub1 error!
open ch_01_sub3 error!
Tue Aug 15 07:23:53 2023 CPU3: ch_01_sub3 timeout, process it with the salvage mode
open ch_01_sub2 error!
Tue Aug 15 07:23:53 2023 CPU1: running on ch_01_sub4
Tue Aug 15 07:23:53 2023 CPU4: running on ch_01_sub5
open ch_01_sub4 error!
Tue Aug 15 07:23:53 2023 CPU1: ch_01_sub4 timeout, process it with the salvage mode
open ch_01_sub5 error!
Tue Aug 15 07:23:53 2023 CPU4: ch_01_sub5 timeout, process it with the salvage mode
Tue Aug 15 07:23:53 2023 CPU2: running on ch_02_sub1
open ch_01_sub3 error!
open ch_02_sub1 error!
Tue Aug 15 07:23:53 2023 CPU2: ch_02_sub1 timeout, process it with the salvage mode
open ch_01_sub4 error!
Tue Aug 15 07:23:53 2023 CPU3: running on ch_02_sub2
open ch_01_sub5 error!
open ch_02_sub2 error!
Tue Aug 15 07:23:53 2023 CPU3: ch_02_sub2 timeout, process it with the salvage mode
open ch_02_sub1 error!
Tue Aug 15 07:23:53 2023 CPU1: running on ch_02_sub3
Tue Aug 15 07:23:53 2023 CPU4: running on ch_02_sub4
open ch_02_sub3 error!
Tue Aug 15 07:23:53 2023 CPU1: ch_02_sub3 timeout, process it with the salvage mode
open ch_02_sub4 error!
Tue Aug 15 07:23:53 2023 CPU4: ch_02_sub4 timeout, process it with the salvage mode
Tue Aug 15 07:23:53 2023 CPU2: running on ch_02_sub5
open ch_02_sub2 error!
open ch_02_sub5 error!
Tue Aug 15 07:23:53 2023 CPU2: ch_02_sub5 timeout, process it with the salvage mode
open ch_02_sub3 error!
open ch_02_sub4 error!
Tue Aug 15 07:23:53 2023 CPU3: running on ch_03_sub1
open ch_02_sub5 error!
open ch_03_sub1 error!
Tue Aug 15 07:23:53 2023 CPU3: ch_03_sub1 timeout, process it with the salvage mode
Tue Aug 15 07:23:53 2023 CPU1: running on ch_03_sub2
Tue Aug 15 07:23:53 2023 CPU4: running on ch_03_sub3
open ch_03_sub2 error!
Tue Aug 15 07:23:53 2023 CPU1: ch_03_sub2 timeout, process it with the salvage mode
open ch_03_sub3 error!
...

sequence name:

ch_01
ch_02
ch_03
ch_04
ch_05
ch_06
ch_07
ch_08
ch_09
ch_10
ch_11
...
ch_z

I also tried another format of the sequence name:

ch01
ch02
ch03
ch04
ch05
ch06
ch07
ch08
ch09
ch10
ch11
...
ch_z

but the same error showed again, how can I resolve it?

[oushujun]

The program cannot read the expected sub file. Please make sure you have write access to the folder.

Shujun

[LarsonWang]

Thanks for your help, But it doesn't work after I modified the access settings to that folder and all files as rwxrwxrwx

[MorganeMilin]

Hello,
I encountered the same problem today, although the tool was working fine several months ago.
I don't know if a solution was found previously but if it helps, I realized that by reducing the names of my sequences in the fasta file (for example: Species_scaffold_1 --> Sp_scaff_1) the analysis ended up failing. By reverting to longer sequence names, the analysis started to work perfectly.

[ArthurSilver]

I also encountered the same problem, this problem maybe caused by different line break in dos and linux system, which make the program cannot read the newly generated sub file, use dos2unix on origin sequence file can solve this problem.