cellranger error fix GTF

Question

[marco.barr]

Hi everyone,

I'm running CellRanger pipeline to analyze my single-cell data. During the index construction step using mkref, I encounter the following error.

mkref has failed: error building reference package  
 Error while parsing GTF file /home/hg38/Homo_sapiens.GRCh38.112.filtered.gtf
 Invalid contig name encountered on GTF line 6: 1. The FASTA file has contigs:
 ['GL000008.2', 'GL000009.2', 'GL000194.1', 'GL000195.1', 'GL000205.2', 'GL000208.1', 'GL000213.1', 'GL000214.1', 'GL000216.2', 'GL000218.1', 
 'GL000219.1', 'GL000220.1', 'GL000221.1', 'GL000224.1', 'GL000225.1', 'GL000226.1', 'KI270302.1', 'KI270303.1', 'KI270304.1', 'KI270305.1', 
'KI270310.1', 'KI270311.1', 'KI270312.1', 'KI270315.1', 'KI270316.1', 'KI270317.1', 'KI270320.1', 'KI270322.1', 'KI270329.1', 'KI270330.1', 'KI270333.1', 
'KI270334.1', 'KI270335.1', 'KI270336.1', 'KI270337.1', 'KI270338.1', 'KI270340.1', 'KI270362.1', 'KI270363.1', 'KI270364.1', 'KI270366.1', 'KI270371.1', 
'KI270372.1', 'KI270373.1', 'KI270374.1', 'KI270375.1', 'KI270376.1', 'KI270378.1', 'KI270379.1', 'KI270381.1', 'KI270382.1', 'KI270383.1', 'KI270384.1', 
'KI270385.1', 'KI270386.1', 'KI270387.1', 'KI270388.1', 'KI270389.1', 'KI270390.1', 'KI270391.1', 'KI270392.1', 'KI270393.1', 'KI270394.1', 'KI270395.1', 
'KI270396.1', 'KI270411.1', 'KI270412.1', 'KI270414.1', 'KI270417.1', 'KI270418.1', 'KI270419.1', 'KI270420.1', 'KI270422.1', 'KI270423.1', 'KI270424.1', 
'KI270425.1', 'KI270429.1', 'KI270435.1', 'KI270438.1', 'KI270442.1', 'KI270448.1', 'KI270465.1', 'KI270466.1', 'KI270467.1', 'KI270468.1', 'KI270507.1', 
'KI270508.1', 'KI270509.1', 'KI270510.1', 'KI270511.1', 'KI270512.1', 'KI270515.1', 'KI270516.1', 'KI270517.1', 'KI270518.1', 'KI270519.1', 'KI270521.1', 
'KI270522.1', 'KI270528.1', 'KI270529.1', 'KI270530.1', 'KI270538.1', 'KI270539.1', 'KI270544.1', 'KI270548.1', 'KI270579.1', 'KI270580.1', 'KI270581.1', 
'KI270582.1', 'KI270583.1', 'KI270584.1', 'KI270587.1', 'KI270588.1', 'KI270589.1', 'KI270590.1', 'KI270591.1', 'KI270593.1', 'KI270706.1', 'KI270707.1', 
'KI270708.1', 'KI270709.1', 'KI270710.1', 'KI270711.1', 'KI270712.1', 'KI270713.1', 'KI270714.1', 'KI270715.1', 'KI270716.1', 'KI270717.1', 'KI270718.1', 
'KI270719.1', 'KI270720.1', 'KI270721.1', 'KI270722.1', 'KI270723.1', 'KI270724.1', 'KI270725.1', 'KI270726.1', 'KI270727.1', 'KI270728.1', 'KI270729.1', 
'KI270730.1', 'KI270731.1', 'KI270732.1', 'KI270733.1', 'KI270734.1', 'KI270735.1', 'KI270736.1', 'KI270737.1', 'KI270738.1', 'KI270739.1', 'KI270740.1', 
'KI270741.1', 'KI270742.1', 'KI270743.1', 'KI270744.1', 'KI270745.1', 'KI270746.1', 'KI270747.1', 'KI270748.1', 'KI270749.1', 'KI270750.1', 'KI270751.1', 
'KI270752.1', 'KI270753.1', 'KI270754.1', 'KI270755.1', 'KI270756.1', 'KI270757.1', 'chr1', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 
'chr18', 'chr19', 'chr2', 'chr20', 'chr21', 'chr22', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chrM', 'chrX', 'chrY']

Please fix your GTF and start again.

These are the commands I used to generate the filtered file.

cellranger mkgtf \
   /home/hg38/Homo_sapiens.GRCh38.112.gtf \
  /home/hg38/Homo_sapiens.GRCh38.112.filtered.gtf \
 --attribute=gene_biotype:protein_coding

What should I do? Thank you very much for your help.

[GenoMax]

During the index construction step using mkref,

Do you have a pressing reason to roll your own when 10x makes GRCh38 pre-made indexes available here: https://www.10xgenomics.com/support/software/cell-ranger/downloads#reference-downloads