index and meta process error

[teichlab]

index and meta process error

[AndreaLGardner]

I had the same issue and it was solved by changing the delimiter on my data; csv worked great

[mvento]

Hi @Jiam1ng,

Did you fix it? Please, send us the input data if it didn't work.

Best

[Jiam1ng]

Hi Miquel, I'm really sorry for not replying, it's likelly that there is something wrong with my mailbox. I have also send this error to the sequencing company, they re-send me the raw data, and it works fine, so I think there may be some mistakes during the data conveying last time. The error is fixed now, really thanks for you kind help, and sorry again for not replying you immediately. Best regards, Jiaming

…

------------------&nbsp;原始邮件&nbsp;------------------ 发件人:&nbsp;"Miquel"<[email protected]&gt;; 发送时间:&nbsp;2020年2月18日(星期二) 凌晨0:50 收件人:&nbsp;"Teichlab/cellphonedb"<[email protected]&gt;; 抄送:&nbsp;"李嘉明"<[email protected]&gt;;"Mention"<[email protected]&gt;; 主题:&nbsp;Re: [Teichlab/cellphonedb] index and meta process error (#131) Hi @Jiam1ng, Did you fix it? Please, send us the input data if it didn't work. Best — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[mvento]

Hi @Jiam1ng,

Perfect! Thanks for using CellPhoneDB.

Best

[wangjiawen2013]

I had the same issue and it was solved by changing the delimiter on my data; csv worked great

I met this error and how to change the delimiter of my meta.csv? I rename meta.csv to meta.txt, then it worked.

[PernilleYR]

I have the same issue, I tried both .txt or .csv and it doesn't solve the problem.
Weirdly it works perfectly fine with other dataset that I processed exactly the same way.
Any idea...?

Here is the error:
[ ][CORE][09/04/21-15:33:30][INFO] Launching Method cpdb_statistical_analysis_launcher
[ ][APP][09/04/21-15:33:30][ERROR] Unexpected error
Traceback (most recent call last):
File "/Users/pernillerainer/cpdb/lib/python3.7/site-packages/cellphonedb/src/core/preprocessors/method_preprocessors.py", line 28, in meta_preprocessor
meta = pd.DataFrame(data={'cell_type': meta_raw.iloc[:, 1]})
File "/Users/pernillerainer/cpdb/lib/python3.7/site-packages/pandas/core/indexing.py", line 873, in getitem
return self._getitem_tuple(key)
File "/Users/pernillerainer/cpdb/lib/python3.7/site-packages/pandas/core/indexing.py", line 1443, in _getitem_tuple
self._has_valid_tuple(tup)
File "/Users/pernillerainer/cpdb/lib/python3.7/site-packages/pandas/core/indexing.py", line 702, in _has_valid_tuple
self._validate_key(k, i)
File "/Users/pernillerainer/cpdb/lib/python3.7/site-packages/pandas/core/indexing.py", line 1352, in _validate_key
self._validate_integer(key, axis)
File "/Users/pernillerainer/cpdb/lib/python3.7/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

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/pernillerainer/cpdb/lib/python3.7/site-packages/cellphonedb/src/api_endpoints/terminal_api/method_terminal_api_endpoints/method_terminal_commands.py", line 144, in statistical_analysis
subsampler,
File "/Users/pernillerainer/cpdb/lib/python3.7/site-packages/cellphonedb/src/local_launchers/local_method_launcher.py", line 64, in cpdb_statistical_analysis_local_method_launcher
subsampler
File "/Users/pernillerainer/cpdb/lib/python3.7/site-packages/cellphonedb/src/core/methods/method_launcher.py", line 50, in cpdb_statistical_analysis_launcher
meta = method_preprocessors.meta_preprocessor(raw_meta)
File "/Users/pernillerainer/cpdb/lib/python3.7/site-packages/cellphonedb/src/core/preprocessors/method_preprocessors.py", line 35, in meta_preprocessor
raise ProcessMetaException
cellphonedb.src.core.exceptions.ProcessMetaException.ProcessMetaException: Error processing Meta data

Thanks!

Best

[prete]

Hi @PernilleYR could you please provide:

• the command you used to launch CellphoneDB
• your meta file or a sample of it

Thanks!

[PernilleYR]

Hi @prete,

Thanks for your answer!

Here is a sample of the metadata:
metadata_example.txt

And the command:
cellphonedb method statistical_analysis data/metadata_example.txt data/normdata_EP0.csv --output-path EP0/

I also tried to use a .csv but it also didn't work, even if I tried other datasets and it worked perfectly

Thank you so much for having a look, let me know if you need more info,

Best,

Pernille

[Genki-YAN]

I also met this error and checked my files. I found there was a line which not split by a tab.