Open allenk42 opened 1 year ago
I ran into the same issue. For me, it was caused by two problems: 1) a permissions issue with the fasta36 tool. I updated the permissions with chmod
and the tool ran the test successfully. 2) a non-fasta file in the --input
folder directory. The tool ran successfully after removing that file
I used chmod
to change the permission status of fasta36. But that error goes on, "FileNotFoundError: [Errno 2] No such file or directory: 'output_cmscan.txt'"
Creating` folders if necessary...
Running CRISPR array search, it may take a while...
Running CRISPR cas search, it may take a while...
Working with 1 files
Working with file 1 - AAAIBU010000002.fasta
1. Searching for anti repeats
2. Filtering Anti-repeats
3. Forming initial TracrRNA candidates
4. Improving the results using CRISPRRNA-TracrRNA interaction prediction
5. Searching for the terminator sequences
6. Searching the hits with the provided tail model
Traceback (most recent call last):
File "CRISPRtracrRNA.py", line 46, in <module>
main()
File "CRISPRtracrRNA.py", line 36, in main
dict_weights=dict_weights)
File "/home/kk/CRISPRtracrRNA/modules/pipelines.py", line 35, in __init__
self._pipeline_run()
File "/home/kk/CRISPRtracrRNA/modules/pipelines.py", line 142, in _pipeline_run
cm_scan_on_candidates = CMScanOnCandidates(all_tracr_sequences_global_window, self.hmm_model)
File "/home/kk/CRISPRtracrRNA/modules/hmm_model_run.py", line 18, in __init__
self._parse_result_file()
File "/home/kk/CRISPRtracrRNA/modules/hmm_model_run.py", line 65, in _parse_result_file
with open("output_cmscan.txt") as f:
FileNotFoundError: [Errno 2] No such file or directory: 'output_cmscan.txt'
I had the same issue, this can be resolved by using chmod
on all of their binaries and executables.
Thanks very much! It really worked!i😁
Could you tell me detail about · using chmod on all of their binaries and executables.·? because I use ·chmod a+x ./tools·, there are still errors like above.
You can try "chmod 777" with all the files in ./CRISPRtracrRNA
hi @allenk42
I have encountered the same problem as you, I used your method, use chmod -R 777 *
or chmod -R 777 ./CRISPRtracrRNA
All my files in this folder are -rwxrwxrwx
. But unable to solve my problem. Here is my usage code and error report.
python CRISPRtracrRNA.py --input_folder cas14input/ --output_folder cas14output/ --output_summary_file cas14_result.csv --model_type V --perform_type_v_anti_repeat_analysis ture
Running CRISPR array search, it may take a while...
Running CRISPR cas search, it may take a while...
Working with 3 files
Working with file 1 - cas14a1.fasta
1. Searching for anti repeats
2. Filtering Anti-repeats
3. Forming initial TracrRNA candidates
4. Improving the results using CRISPRRNA-TracrRNA interaction prediction
5. Searching for the terminator sequences
6. Searching the hits with the provided tail model
Traceback (most recent call last):
File "CRISPRtracrRNA.py", line 46, in <module>
main()
File "CRISPRtracrRNA.py", line 36, in main
dict_weights=dict_weights)
File "/mnt/f/生信数据/CRISPRtracrRNA/modules/pipelines.py", line 35, in __init__
self._pipeline_run()
File "/mnt/f/生信数据/CRISPRtracrRNA/modules/pipelines.py", line 142, in _pipeline_run
cm_scan_on_candidates = CMScanOnCandidates(all_tracr_sequences_global_window, self.hmm_model)
File "/mnt/f/生信数据/CRISPRtracrRNA/modules/hmm_model_run.py", line 18, in __init__
self._parse_result_file()
File "/mnt/f/生信数据/CRISPRtracrRNA/modules/hmm_model_run.py", line 65, in _parse_result_file
with open("output_cmscan.txt") as f:
FileNotFoundError: [Errno 2] No such file or directory: 'output_cmscan.txt'
Anyway, thank you for your help!
首先试试把文件夹上的中文都改成英文吧😂
大佬,改了还是没用。头疼了😭
Creating folders if necessary...
Running CRISPR array search, it may take a while...
Running CRISPR cas search, it may take a while...
Working with 3 files
Working with file 1 - cas14a1.fasta
1. Searching for anti repeats
2. Filtering Anti-repeats
3. Forming initial TracrRNA candidates
4. Improving the results using CRISPRRNA-TracrRNA interaction prediction
5. Searching for the terminator sequences
6. Searching the hits with the provided tail model
Traceback (most recent call last):
File "CRISPRtracrRNA.py", line 46, in <module>
main()
File "CRISPRtracrRNA.py", line 36, in main
dict_weights=dict_weights)
File "/mnt/f/Bioinformatics_data/CRISPRtracrRNA/modules/pipelines.py", line 35, in __init__
self._pipeline_run()
File "/mnt/f/Bioinformatics_data/CRISPRtracrRNA/modules/pipelines.py", line 142, in _pipeline_run
cm_scan_on_candidates = CMScanOnCandidates(all_tracr_sequences_global_window, self.hmm_model)
File "/mnt/f/Bioinformatics_data/CRISPRtracrRNA/modules/hmm_model_run.py", line 18, in __init__
self._parse_result_file()
File "/mnt/f/Bioinformatics_data/CRISPRtracrRNA/modules/hmm_model_run.py", line 65, in _parse_result_file
with open("output_cmscan.txt") as f:
FileNotFoundError: [Errno 2] No such file or directory: 'output_cmscan.txt'
Please allow me to respond in Chinese. 根据我的使用经验来看,这个报错是不影响最终结果的。这个结果报错,更多的是在你的序列中没有找到适合条件的arry信息。
@Golden-proteogenomics
Thanks for your help, I will test with more sequences of cas12 system next. 谢谢大佬,我再用别的cas12序列试试。
the same problem happens to me, so could you help me !!!!
Hi, I got an error: "FileNotFoundError: [Errno 2] No such file or directory: 'output_cmscan.txt'". How can I get this problem solved ?