FileNotFoundError: [Errno 2] No such file or directory: 'output_cmscan.txt'

[allenk42]

Hi, I got an error: "FileNotFoundError: [Errno 2] No such file or directory: 'output_cmscan.txt'".
How can I get this problem solved ?

[sbenler]

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

[allenk42]

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'

[lawrence-ip]

I had the same issue, this can be resolved by using chmod on all of their binaries and executables.

[allenk42]

Thanks very much! It really worked!i😁

[Golden-proteogenomics]

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.

[allenk42]

You can try "chmod 777" with all the files in ./CRISPRtracrRNA

[zhp2333]

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!

[allenk42]

首先试试把文件夹上的中文都改成英文吧😂

[zhp2333]

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'

[Golden-proteogenomics]

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。

[zhp2333]

@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。

[N-yating]

the same problem happens to me, so could you help me !!!!