Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error in running python3 find_RCRJ_and_classify.py -y config.yaml #12

Open
Tanv1 opened this issue Feb 10, 2021 · 0 comments
Open

Error in running python3 find_RCRJ_and_classify.py -y config.yaml #12

Tanv1 opened this issue Feb 10, 2021 · 0 comments

Comments

@Tanv1
Copy link

Tanv1 commented Feb 10, 2021

15447
15448
15449
15450
15451
Error in (function (edges, n = max(edges), directed = TRUE) :
At type_indexededgelist.c:117 : cannot create empty graph with negative number of vertices, Invalid value
Calls: classification -> createNet -> graph -> do.call ->
In addition: Warning message:
In max(edges) : no non-missing arguments to max; returning -Inf
Execution halted
Classify successfully!
sed: can't read /path/to/my_directory/CircCode_tem/ERR45678Aligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa: No such file or directory
Traceback (most recent call last):
File "find_RCRJ_and_classify.py", line 369, in
main()
File "find_RCRJ_and_classify.py", line 355, in main
classify(coding_seq,
File "find_RCRJ_and_classify.py", line 102, in classify
seqs = SeqIO.parse(final_trans_file, 'fasta')
File "/home/.conda/envs/circcode_env/lib/python3.8/site-packages/Bio/SeqIO/init.py", line 607, in parse
return iterator_generator(handle)
File "/home/.conda/envs/circcode_env/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 183, in init
super().init(source, mode="t", fmt="Fasta")
File "/home/.conda/envs/circcode_env/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 47, in init
self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: '/path/to/my_directory/CircCode_tem/ERR45678Aligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa'

Help needed!

@Tanv1 Tanv1 changed the title BASiNET and Biostrings installation error in linux environment Error in running python3 find_RCRJ_and_classify.py -y config.yaml Feb 26, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant