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yangence / circfull

a tool to detect and quantify full-length circRNA isoforms from circFL-seq
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IndexError: single positional indexer is out-of-bounds #7

Closed koosle closed 2 years ago

koosle commented 2 years ago

Dear author, Hi! When I run the circfull, there was a bug about that "IndexError: single positional indexer is out-of-bounds". The version of circfull is 0.0.8. Some samples could be all done, but others has the above bug. Could you give me some suggestions? Thanks a lot!

koosle commented 2 years ago

The bug as the list:

`Filter BS: filterBS

2022-06-29 10:36:09

Construct FL-circRNA: constructFL

2022-06-29 10:37:45

Adjust FL-circRNA: adjFL

2022-06-29 10:47:06

Adjust mistaken circRNA: circSeq

2022-06-29 10:47:29

Annotate circRNA: annotateNormal

2022-06-29 10:47:44

Analyze fusion circRNA: fusionFq

2022-06-29 10:47:49

Re-alignment to pseudo reference: detectBS_fusion1

2022-06-29 10:48:11

Filter fusion BS: filterBS_fusion1

2022-06-29 10:52:46

Construct fusion FL-circRNA: fusion1ConstructFL

2022-06-29 10:55:09

Adjust fusion FL-circRNA: fusion1AdjFL

2022-06-29 11:05:03

Annotate fusion FL-circRNA: fusion1CombinFL Traceback (most recent call last): File "/home/jinwen/miniconda3/envs/nanopore/bin/circfull", line 33, in sys.exit(load_entry_point('circfull==0.0.8', 'console_scripts', 'circfull')()) File "/home/jinwen/miniconda3/envs/nanopore/lib/python3.6/site-packages/circfull-0.0.8-py3.6.egg/circfull/circFL_main.py", line 37, in main File "/home/jinwen/miniconda3/envs/nanopore/lib/python3.6/site-packages/circfull-0.0.8-py3.6.egg/circfull/RG.py", line 127, in RG File "/home/jinwen/miniconda3/envs/nanopore/lib/python3.6/site-packages/circfull-0.0.8-py3.6.egg/circfull/RG_fusion1CombinFL.py", line 182, in fusion1CombinFL File "/home/jinwen/miniconda3/envs/nanopore/lib/python3.6/site-packages/pandas/core/indexing.py", line 873, in getitem return self._getitem_tuple(key) File "/home/jinwen/miniconda3/envs/nanopore/lib/python3.6/site-packages/pandas/core/indexing.py", line 1443, in _getitem_tuple self._has_valid_tuple(tup) File "/home/jinwen/miniconda3/envs/nanopore/lib/python3.6/site-packages/pandas/core/indexing.py", line 702, in _has_valid_tuple self._validate_key(k, i) File "/home/jinwen/miniconda3/envs/nanopore/lib/python3.6/site-packages/pandas/core/indexing.py", line 1352, in _validate_key self._validate_integer(key, axis) File "/home/jinwen/miniconda3/envs/nanopore/lib/python3.6/site-packages/pandas/core/indexing.py", line 1437, in _validate_integer raise IndexError("single positional indexer is out-of-bounds") IndexError: single positional indexer is out-of-bounds`

colinliuzelin commented 2 years ago

Hi koosle! Thank you for your feedback. I have some thoughts about this bug but need your file to test it. Could you send me your output files in fusion directory? Thanks

koosle commented 2 years ago

Hi koosle! Thank you for your feedback. I have some thoughts about this bug but need your file to test it. Could you send me your output files in fusion directory? Thanks

All files of “fusion” folder?

colinliuzelin commented 2 years ago

A compressed package of fusion directory. I think its size is small.

koosle commented 2 years ago

A compressed package of fusion directory. I think its size is small.

The file directory is (https://github.com/koosle/tmp) , you can download it.

colinliuzelin commented 2 years ago

Hi koosle! I have checked your file. It seems some of reads were mapped on reference patches, such as GL582976.1, GL949752.1. I suggest you to only keep chromosomes starting with 'chr' in your reference geome and re-run circfull.

koosle commented 2 years ago

Thanks for your suggestion. I had tried your method again, but it was still left the same problem. Is it possible that these samples do not have fusion genes?

colinliuzelin commented 2 years ago

I agree it is possible that these samples do not have fusion genes. However, circfull will pass through this part if there is no fusion circRNA. Could you send me the compressed package of fusion directory without reference patches? I want to figure out this problem. Thank you!

koosle commented 2 years ago

The file directory is (https://github.com/koosle/temp2) . Thank you again!

colinliuzelin commented 2 years ago

Hi koosle! I have fixed the bug. But before I release the fixed version, could you help me check it with your data? I have push the newest version at develop branch. For your convenience, you can change your circfull script with the files in the link https://github.com/yangence/circfull/tree/develop/script/circfull Thank you!

koosle commented 2 years ago

Thanks for your job! I have changed the circfull script with your files and tried again, but the same bug still existed.

gnilihzeux commented 2 years ago

@colinliuzelin Hi, have you solve this? I suffered the same problem.

colinliuzelin commented 2 years ago

Sorry for the late response. Can you provide your reference genome and GTF annotation file? And the error information of this time. Thank you!

gnilihzeux commented 2 years ago

The genome and gtf are from GENCODE GRCh37.p13 and they are all about 'Chr' information without paches.

The error information :

Annotate fusion FL-circRNA: fusion2CombinFL
Traceback (most recent call last):
  File "/home/gnilihzeux/miniconda3/envs/nano/bin/circfull", line 33, in <module>
    sys.exit(load_entry_point('circfull==0.0.8', 'console_scripts', 'circfull')())
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/circfull-0.0.8-py3.6.egg/circfull/circFL_main.py", line 37, in main
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/circfull-0.0.8-py3.6.egg/circfull/RG.py", line 153, in RG
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/circfull-0.0.8-py3.6.egg/circfull/RG_fusion2CombinFL.py", line 182, in fusion2CombinFL
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/pandas/core/indexing.py", line 873, in __getitem__
    return self._getitem_tuple(key)
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/pandas/core/indexing.py", line 1443, in _getitem_tuple
    self._has_valid_tuple(tup)
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/pandas/core/indexing.py", line 702, in _has_valid_tuple
    self._validate_key(k, i)
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/pandas/core/indexing.py", line 1352, in _validate_key
    self._validate_integer(key, axis)
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/pandas/core/indexing.py", line 1437, in _validate_integer
    raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds
colinliuzelin commented 2 years ago

The genome and gtf are from GENCODE GRCh37.p13 and they are all about 'Chr' information without paches.

The error information :

Annotate fusion FL-circRNA: fusion2CombinFL
Traceback (most recent call last):
  File "/home/gnilihzeux/miniconda3/envs/nano/bin/circfull", line 33, in <module>
    sys.exit(load_entry_point('circfull==0.0.8', 'console_scripts', 'circfull')())
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/circfull-0.0.8-py3.6.egg/circfull/circFL_main.py", line 37, in main
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/circfull-0.0.8-py3.6.egg/circfull/RG.py", line 153, in RG
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/circfull-0.0.8-py3.6.egg/circfull/RG_fusion2CombinFL.py", line 182, in fusion2CombinFL
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/pandas/core/indexing.py", line 873, in __getitem__
    return self._getitem_tuple(key)
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/pandas/core/indexing.py", line 1443, in _getitem_tuple
    self._has_valid_tuple(tup)
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/pandas/core/indexing.py", line 702, in _has_valid_tuple
    self._validate_key(k, i)
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/pandas/core/indexing.py", line 1352, in _validate_key
    self._validate_integer(key, axis)
  File "/home/gnilihzeux/miniconda3/envs/nano/lib/python3.6/site-packages/pandas/core/indexing.py", line 1437, in _validate_integer
    raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds

Hi! Have you tried these new scripts in https://github.com/yangence/circfull/tree/develop/script/circfull. You can change your circfull script with the files. If you still have the bug, please tell me the error information. Thank you!

gnilihzeux commented 2 years ago

Great, it works. I changed the circfull scripts and re-install them. Thanks a million.