You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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!
The text was updated successfully, but these errors were encountered:
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
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!
The text was updated successfully, but these errors were encountered: