Error when running search_for_sgRNA_illumina.py

[kjshan]

I do have any error when I run this command below and obtain the error

command:

python /lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/site-packages/periscope/scripts/search_for_sgRNA_illumina.py --bam MA104_Alpha.bam --score-cutoff 50 --output-prefix MA104_Alpha --score-cutoff 50 --sample MA104_Alpha --orf-bed /gpfs2/shankj/software/periscope-master/periscope/resources//orf_start.bed --primer-bed /gpfs2/shankj/software/periscope-master/periscope/resources/artic_primers_V1.bed --amplicon-bed /gpfs2/shankj/software/periscope-master/periscope/resources/artic_amplicons_V1.bed --tmp /tmp --threads 1

Error:

2023-02-15 15:28:34,158 - staring periscope 0%| | 0/10 [00:00<?, ?it/s]2023-02-15 15:33:03,688 - Processing 6663791 reads Process Process-1: Traceback (most recent call last): File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/concurrent/futures/process.py", line 181, in _process_worker result=r)) File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/multiprocessing/queues.py", line 347, in put self._writer.send_bytes(obj) File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/multiprocessing/connection.py", line 200, in send_bytes self._send_bytes(m[offset:offset + size]) File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/multiprocessing/connection.py", line 393, in _send_bytes header = struct.pack("!i", n) struct.error: 'i' format requires -2147483648 <= number <= 2147483647 0%| | 0/10 [37:39<?, ?it/s] Traceback (most recent call last): File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/site-packages/periscope/scripts/search_for_sgRNA_illumina.py", line 393, in periscope = main(args) File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/site-packages/periscope/scripts/search_for_sgRNA_illumina.py", line 309, in main workers=int(args.threads) File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/site-packages/periscope/scripts/search_for_sgRNA_illumina.py", line 281, in multiprocessing res = list(tqdm(ex.map(func, args), total=len(args))) File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/site-packages/tqdm/std.py", line 1129, in iter for obj in iterable: File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/concurrent/futures/process.py", line 366, in _chain_from_iterable_of_lists for element in iterable: File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/concurrent/futures/_base.py", line 586, in result_iterator yield fs.pop().result() File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/concurrent/futures/_base.py", line 432, in result return self.get_result() File "/lustre/user/lulab/shankj/miniconda3/envs/periscope/lib/python3.6/concurrent/futures/_base.py", line 384, in get_result raise self._exception concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.

Could you guys be friendly to help me? Thanks for your time

[mbdabrowska1]

Hi, could you try using more threads to see if this helps the issue?