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I'm using CircCode, but every time I am facing the same problem. I would appreciate any help to resolve this issue:
When I run - find_RCRJ_and_classify.py it gives following error: 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 /userdata/lab/RPFAligned.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/lab/.conda/envs/circcode_env/lib/python3.8/site-packages/Bio/SeqIO/init.py", line 607, in parse
return iterator_generator(handle)
File "/home/lab/.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/lab/.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: '/userdata/lab/RPFAligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa'
Please note that -
"RPFAligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa" no such file is getting generated after mapping in previous step.
Could you help me figure out this? Thanks in advance.
Best,
Tanvi
The text was updated successfully, but these errors were encountered:
Execution halted
sed: can't read /home/leelee/tools/circcode/CircCode-master/test/LC501_tumor_RPFAligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa: No such file or directory
find_RCRJ_and_classify.py:327: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
fileload = yaml.load(file)
/home/leelee/tools/circcode/CircCode-master/test/test.fa
Classify successfully!
Traceback (most recent call last):
File "find_RCRJ_and_classify.py", line 369, in <module>
main()
File "find_RCRJ_and_classify.py", line 363, in main
use_classify)
File "find_RCRJ_and_classify.py", line 102, in classify
seqs = SeqIO.parse(final_trans_file, 'fasta')
File "/home/leelee/miniconda3/envs/circcode/lib/python3.7/site-packages/Bio/SeqIO/__init__.py", line 605, in parse
return iterator_generator(handle)
File "/home/leelee/miniconda3/envs/circcode/lib/python3.7/site-packages/Bio/SeqIO/FastaIO.py", line 183, in __init__
super().__init__(source, mode="t", fmt="Fasta")
File "/home/leelee/miniconda3/envs/circcode/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py", line 48, in __init__
self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: '/home/leelee/tools/circcode/CircCode-master/test/LC501_tumor_RPFAligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa'
Hey
I'm using CircCode, but every time I am facing the same problem. I would appreciate any help to resolve this issue:
When I run - find_RCRJ_and_classify.py it gives following error:
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 /userdata/lab/RPFAligned.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/lab/.conda/envs/circcode_env/lib/python3.8/site-packages/Bio/SeqIO/init.py", line 607, in parse
return iterator_generator(handle)
File "/home/lab/.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/lab/.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: '/userdata/lab/RPFAligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa'
Please note that -
"RPFAligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa" no such file is getting generated after mapping in previous step.
Could you help me figure out this? Thanks in advance.
Best,
Tanvi
The text was updated successfully, but these errors were encountered: