ERROR: Identify TIR candidates from scratch

[Lee951108]

Dear Dr. Ou， I got an error，when i run the EDTA.pl for a plant genome. Please help me to figure this out.

Tue Jul 16 11:17:49 CST 2024 EDTA_raw: Check dependencies, prepare working directories.

Tue Jul 16 11:18:05 CST 2024 Start to find LTR candidates.

Tue Jul 16 11:18:05 CST 2024 Existing result file Zm-B73-REFERENCE-NAM-5.0.fa.mod.LTR.raw.fa found! Will keep this file without rerunning this module. Please specify --overwrite 1 if you want to rerun this module.

Tue Jul 16 11:18:06 CST 2024 Finish finding LTR candidates.

Tue Jul 16 11:18:06 CST 2024 Start to find SINE candidates.

Tue Jul 16 11:18:06 CST 2024 Existing result file Seed_SINE.fa found! Will keep this file without rerunning this module. Please specify --overwrite 1 if you want to rerun AnnoSINE_v2.

Tue Jul 16 11:18:14 CST 2024 Finish finding SINE candidates.

Tue Jul 16 11:18:14 CST 2024 Start to find LINE candidates.

Tue Jul 16 11:18:14 CST 2024 Existing result file Zm-B73-REFERENCE-NAM-5.0.fa.mod-families.fa found! Will keep this file without rerunning this module. Please specify --overwrite 1 if you want to rerun this module.

Use of uninitialized value in string ne at /share/home/caas_lws/software/EDTA-2.2.0/util/cleanup_misclas.pl line 61, line 176. Use of uninitialized value within %lib in string ne at /share/home/caas_lws/software/EDTA-2.2.0/util/cleanup_misclas.pl line 61, line 176. Tue Jul 16 11:18:20 CST 2024 Finish finding LINE candidates.

Tue Jul 16 11:18:20 CST 2024 Start to find TIR candidates.

Tue Jul 16 11:18:20 CST 2024 Identify TIR candidates from scratch.

Species: Maize Process ForkPoolWorker-44: Process ForkPoolWorker-43: Process ForkPoolWorker-41: Process ForkPoolWorker-42: Process ForkPoolWorker-40: Process ForkPoolWorker-39: Process ForkPoolWorker-38: Process ForkPoolWorker-37: Traceback (most recent call last): File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/pool.py", line 114, in worker task = get() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/queues.py", line 365, in get res = self._reader.recv_bytes() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/connection.py", line 216, in recv_bytes buf = self._recv_bytes(maxlength) File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/connection.py", line 414, in _recv_bytes buf = self._recv(4) File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/connection.py", line 379, in _recv chunk = read(handle, remaining) KeyboardInterrupt Traceback (most recent call last): File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(*self._args, *self._kwargs) File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/pool.py", line 114, in worker task = get() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/queues.py", line 364, in get with self._rlock: File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() KeyboardInterrupt Traceback (most recent call last): Traceback (most recent call last): File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(self._args, self._kwargs) File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/pool.py", line 114, in worker task = get() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/queues.py", line 364, in get with self._rlock: File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/pool.py", line 114, in worker task = get() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/queues.py", line 364, in get with self._rlock: Traceback (most recent call last): File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() KeyboardInterrupt Traceback (most recent call last): KeyboardInterrupt Traceback (most recent call last): File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() Traceback (most recent call last): File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(*self._args, *self._kwargs) File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/pool.py", line 114, in worker task = get() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(self._args, self._kwargs) File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/queues.py", line 364, in get with self._rlock: File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/pool.py", line 114, in worker task = get() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(*self._args, *self._kwargs) File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/queues.py", line 364, in get with self._rlock: File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/pool.py", line 114, in worker task = get() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(self._args, **self._kwargs) File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() KeyboardInterrupt File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/queues.py", line 364, in get with self._rlock: File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/pool.py", line 114, in worker task = get() File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() KeyboardInterrupt File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/queues.py", line 364, in get with self._rlock: File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() KeyboardInterrupt KeyboardInterrupt Exception ignored in: <function _releaseLock at 0x2b577292dea0> Traceback (most recent call last): File "/share/home/caas_lws/miniconda3/envs/EDTA/lib/python3.10/logging/init.py", line 228, in _releaseLock def _releaseLock(): KeyboardInterrupt: Job 11314233 stderr output:

[santoshdu]

Dear Dr. Ou， I also got similar error，when i run the EDTA.pl for a plant genome. Please help me to figure this out.

[FayeFang17]

May I ask what method did you use to install EDTA?

[Lee951108]

I reinstall the EDTA. No error occur. Thanks!