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"Fail to open input file..." Error #11

Open alicerlam opened 1 year ago

alicerlam commented 1 year ago

Hi!

When I try running CytoSig through command line, I consistently get a "Fail to open input file" error regardless of multiple file formats I've tried (exporting as csv/xls, exporting as cell ranger output, exporting as gz, all from Seurat). I get the same error when trying to run "Example 1" with the test data provided in the tests folder. Attached is an image of the error given when I try to run the example:

Screenshot 2023-06-28 at 01 37 56

Do you have any suggestions to address this? Thanks in advance!

data2intelligence commented 1 year ago

Hi, Alice,

This is really weird. I just run the command on my laptop, everything looks good. One potential reason is some character encoding difference if you use other language input.

Can you CD into the CytoSig project folder, then copy and paste the following line into your terminal and try again?

CytoSig_run.py -i tests/GSE147507.diff.gz -o tests/output_test -e 1

Sincerely, Peng

On Jun 28, 2023, at 1:38 AM, Alice Lam @.***> wrote:

Hi!

When I try running CytoSig through command line, I consistently get a "Fail to open input file" error regardless of multiple file formats I've tried (exporting as csv/xls, exporting as cell ranger output, exporting as gz, all from Seurat). I get the same error when trying to run "Example 1" with the test data provided in the tests folder. Attached is an image of the error given when I try to run the example:

[Screenshot 2023-06-28 at 01 37 56]https://user-images.githubusercontent.com/37192537/249363342-e1a2314e-f83e-4432-abd0-9b694ca79f25.png

Do you have any suggestions to address this? Thanks in advance!

— Reply to this email directly, view it on GitHubhttps://github.com/data2intelligence/CytoSig/issues/11, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQRREF3LIJ7AI4IW6ZFE4FDXNO7NZANCNFSM6AAAAAAZWQQRPU. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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alicerlam commented 1 year ago

Hi Peng,

Thank you for your response! I've tried copying the line you suggested, which gives the same result as above. I am currently in the cytosig directory (same as first screenshot) and my laptop is set to English (US).

data2intelligence commented 1 year ago

Hi, Lam,

This is very weird. But don’t worry, let me help you in another way:

Can you check “Usage 3, through Docker:” in the README page, and let me know if the docker works for you?

Sent from my iPhone

On Jun 28, 2023, at 5:39 PM, Alice Lam @.***> wrote:



Hi Peng,

Thank you for your response! I've tried copying the line you suggested, which gives the same result as above. I am currently in the cytosig directory (same as first screenshot) and my laptop is set to English (US).

— Reply to this email directly, view it on GitHubhttps://github.com/data2intelligence/CytoSig/issues/11#issuecomment-1612142713, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQRREFZOCUU2MMPFP27MT43XNSQBLANCNFSM6AAAAAAZWQQRPU. You are receiving this because you commented.Message ID: @.***>

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

LuckyLovesParis commented 2 months ago

Hi,

I also encounter an issue of :"Fail to open input file GSE139829_sample/GSM4147093UMM059,GSM4147096UMM063,GSM4147099UMM066" run with CytoSig_run.py using Example 2. Example 1 work perfectly OK. I run it in conda environment. I have been struggling with issue for several days, could you please help with this?

Many thanks!

chenziyi commented 2 months ago

A same problem was also observed in my linux server when I run the command "CytoSig_run.py -i /data/T_cell/RNA.counts/Tcell -o /data/T_cell -e 1 minimum_read_count 200" in both shell and R, python. Could you please help me for this issue. Thanks a lot.

data2intelligence commented 2 weeks ago

Dear All, I just corrected a bug of CytoSig due to the differences of new python versions after Python 3.8 to 3.9, 10, or 11. Could you please try again?