Error in "cellranger mkref"

[grimwoo]

Thanks for the development of cellranger-7.1.0. I successfully created the count files of human, mouse, and etc. via "cellranger count" command. However, I encountered an error in making genome reference for axolotl (salamander).

The gtf file was downloaded from https://www.axolotl-omics.org/dl/AmexT_v47-AmexG_v6.0-DD.gtf.gz.
The fa file was downloaded from https://www.axolotl-omics.org/dl/AmexG_v6.0-DD.fa.gz.

I tried to fix the gtf file according to your recommendation:
https://kb.10xgenomics.com/hc/en-us/articles/4707448154381-Common-mkref-formatting-errors-when-building-custom-reference-from-NCBI-UCSC-or-RefSeq-genomes
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references#ref-pack

Using the filtered gtf file ("AmexT_v47-AmexG_v6.0-DD_fittered.gtf"), I still encountered error after the following second command.

cellranger mkgtf \
  AmexT_v47-AmexG_v6.0-DD_fittered.gtf \
  AmexT_v47-AmexG_v6.0-DD.filtered.again.gtf \
  --attribute=gene_biotype:protein_coding

cellranger mkref \
  --genome=Axolotl_genome \
  --fasta=AmexG_v6.0-DD.fa \
  --genes=AmexT_v47-AmexG_v6.0-DD.filtered.again.gtf

Indexing genome FASTA file...
...done

Writing genes GTF file into reference folder...
WARNING: The following transcripts appear on multiple chromosomes in the GTF:
TMEM11
SGMS1
HTR3E
SELENOO
SYNJ2BP
NXPE2
GNGT1
ARPC1A
MYH2
N/A
PRDM9

This can indicate a problem with the reference or annotations. Only the first chromosome will be counted.
...done

mkref has failed: error building reference package
Error detected in GTF file: Previous 'exon' entry for transcript_id ACER1 had strand == (-), but 'transcript' entry has strand == (+)

Could you please help me to produce a reference for axolotl (salamander).

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