velocyte `run10x` error: Genome annotation gtf file is not sorted correctly!

[jiangpuxuan]

I use my customized .gtf file to run 10x scRNA pipeline and everything is OK. However, when it came to velocyte run10x, here is an error:

OSError: Genome annotation gtf file is not sorted correctly! Run the following command:
sort -k1,1 -k7,7 -k4,4n -o [GTF_OUTFILE] [GTF_INFILE]

I ran the sort -k1,1 -k7,7 -k4,4n -o [GTF_OUTFILE] [GTF_INFILE] but it failed again. I did not use the -m parameter, so the format of mask.gtf did nothing with this run10x problem.

Here is head my.gtf:

"1"     "ensembl"       "gene"  20431   58833   "."     "-"     "."     "gene_id IGDB00001; gene_name IGDB00001"
"1"     "ensembl"       "gene"  92003   119620  "."     "-"     "."     "gene_id IGDB00002; gene_name IGDB00002"
"1"     "ensembl"       "gene"  103603  105216  "."     "+"     "."     "gene_id IGDB00003; gene_name IGDB00003"
"1"     "ensembl"       "gene"  121139  134255  "."     "-"     "."     "gene_id IGDB00004; gene_name IGDB00004"
"1"     "ensembl"       "gene"  121795  124788  "."     "+"     "."     "gene_id IGDB00005; gene_name IGDB00005"
"1"     "ensembl"       "gene"  152322  157371  "."     "+"     "."     "gene_id IGDB00006; gene_name IGDB00006"
"1"     "ensembl"       "gene"  153964  160887  "."     "-"     "."     "gene_id IGDB00007; gene_name IGDB00007"
"1"     "ensembl"       "gene"  202049  207179  "."     "+"     "."     "gene_id IGDB00008; gene_name IGDB00008"
"1"     "ensembl"       "gene"  203029  221904  "."     "-"     "."     "gene_id IGDB00009; gene_name IGDB00009"
"1"     "ensembl"       "gene"  278769  280886  "."     "+"     "."     "gene_id IGDB00010; gene_name IGDB00010"

Here is my.gtf after sort -k1,1 -k7,7 -k4,4n -o [GTF_OUTFILE] [GTF_INFILE]:

"000062F"       "StringTie"     "exon"  8693    11960   "1000.00"       "+"     "."     "gene_id 10297.1; transcript_id IGDB10297.1"
"000062F"       "StringTie"     "gene"  8693    11960   "1000.00"       "+"     "."     "gene_id IGDB10297; gene_name IGDB10297"
"000062F"       "StringTie"     "transcript"    8693    11960   "1000.00"       "+"     "."     "gene_id IGDB10297; transcript_id IGDB10297.1; gene_id IGDB10297; transcript_id IGDB10297.1"
"000062F"       "StringTie"     "exon"  1468    2226    "1000.00"       "-"     "."     "gene_id 10295.1; transcript_id IGDB10295.1"
"000062F"       "StringTie"     "gene"  1468    2226    "1000.00"       "-"     "."     "gene_id IGDB10295; gene_name IGDB10295"
"000062F"       "StringTie"     "transcript"    1468    2226    "1000.00"       "-"     "."     "gene_id IGDB10295; transcript_id IGDB10295.1; gene_id IGDB10295; transcript_id IGDB10295.1"
"000062F"       "StringTie"     "exon"  7600    7807    "1000.00"       "-"     "."     "gene_id 10296.1; transcript_id IGDB10296.1"
"000062F"       "StringTie"     "gene"  7600    7807    "1000.00"       "-"     "."     "gene_id IGDB10296; gene_name IGDB10296"
"000062F"       "StringTie"     "transcript"    7600    7807    "1000.00"       "-"     "."     "gene_id IGDB10296; transcript_id IGDB10296.1; gene_id IGDB10296; transcript_id IGDB10296.1"
"000076F"       "StringTie"     "exon"  15532   15624   "1000.00"       "+"     "."     "gene_id 10298.1; transcript_id IGDB10298.1"

[yah-ox]

Hi, I'm having the same issue. My gtf file was said to be not sorted correctly and the same code was provided to be run. After running the "sort -k1,1 -k7,7 -k4,4n -o [GTF_OUTFILE] [GTF_INFILE]", the new gtf was used to run but the same error information showed again. May i know have you figured it out?

Best, yh

[jiangpuxuan]

Hi, I'm having the same issue. My gtf file was said to be not sorted correctly and the same code was provided to be run. After running the "sort -k1,1 -k7,7 -k4,4n -o [GTF_OUTFILE] [GTF_INFILE]", the new gtf was used to run but the same error information showed again. May i know have you figured it out?

Best, yh

Sorry，I have not solved it......