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gaolabtools / scNanoGPS

Single cell Nanopore sequencing data for Genotype and Phenotype
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error message after "5.2 Single cell isoform profile" is finished #27

Closed myanofgintmd closed 7 months ago

myanofgintmd commented 7 months ago

Hello Cheng-kai, I come to the "5.2 Single cell isoform profile". After the process is finished, there comes error messege. Is this a problem?

Batch LIQA jobs finished !

Time stamp: Tue, 16 Apr 2024 17:51:06

Time elapse: 0 : 23 : 15.58
Traceback (most recent call last):
  File "/home/minoruyano/opt/local/scNanoGPS/reporter_isoform.py", line 201, in <module>
    res_tb[CB].update({options.tx_mapping[line_list[1]] + '_' + line_list[1]: line_list[2]})
                       ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
KeyError: 'ENST00000639447'

Best regards, Minoru

shiauck commented 7 months ago

Hi Minoru,

This error is due to no isoform detection in a particular single cell. When compiling all the single cell isoform results into isoform matrix, it generates the error. Please check if you got isoform matrix. Thanks.

Regards, Cheng-Kai

myanofgintmd commented 7 months ago

Hi Cheng-Kai,

Thank you reply for my post. I understand that the error is because of no isoform in a paticular single cell. Now, this trouble has been solved.

Reviwing the situation when I had got the error message, I found as below. I have got the error message when I set "--min_gene_no 1" at the previous reporter_expression.py process. I set this "--min_gene_no" option intentionally in order to get all CB data at this point even though they are with very small number of reads .

According to your advice, I redo the reporter_expression.py process without the option, so that the Minimal number of gene per cell became default "Default: 300". Then, CBs with very small number were eliminated at the reporter_expression.py process, then the error message did not come up at this reporter_isoform.py process.

Best regards, Minoru