Detect 0 cells expressed at least 200 genes, results output to out.csv

[ruocensong]

Sample = out Reference annotation index = mm10.exclusive.idx Minimum number of genes required = 200 Minimum number of counts required = None Number of threads = 1

INFO : Loading the genome annotation index... 2022-11-17 10:34:45 INFO : Loaded 'mm10.exclusive.idx' binary file with 3900779 items ['1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '3', '4', '5', '6', '7', '8', '9', 'M', 'X', 'Y'] INFO : Finished loading the genome annotation index... 2022-11-17 10:35:33

INFO : Processing BAM/SAM files ...2022-11-17 10:35:33 INFO : Input SAM/BAM file appears to be valid CR UR good

sh: 1: gzip: Exec format error INFO : Done BAM/SAM files processing ...2022-11-17 10:35:39

INFO : Splitting ...2022-11-17 10:35:39 INFO : Executing single thread path INFO : Finished processing sample files 2022-11-17 10:35:39

INFO : Fetching from the annotation index... 2022-11-17 10:35:39 sh: 1: gzip: Exec format error /usr/bin/gunzip: 57: exec: gzip: Exec format error INFO : Done fetching... 2022-11-17 10:35:39

INFO : Calculating expression... 2022-11-17 10:35:39 INFO : Detect 0 cells expressed at least 200 genes, results output to out.csv INFO : Finished calculating expression 2022-11-17 10:35:39 INFO : Done with 0d 0h 0m 53s

I used test.bam to run it. But the results showed detect 0 cells expressed. Does it mean still not working?

[A1aNNN]

@jphe Is this the expected result with the test bam file? I tried editing the scTE script to detect cells expressing at least 1 gene instead of 200, and kept getting the result of 0 cells.

Thanks in advance.

[jphe]

The test bam file is very small, your output is correct.

[A1aNNN]

Thanks for the clarification!