kallisto genomebam error

I am trying to produce bam files to load to igv after kallisto quant with –genobam option.

This is the code that I am using

kallisto quant -i Homo_sapiens.GRCh38.cdna.all.release-100.idx -o $FOLDER -t 12 --genomebam -g Homo_sapiens.GRCh38.100.gtf.gz -c hg38.chrom.sizes_clean_tab.txt --rf-stranded ${FILES[$i]} ${FILES[$i+1]}

My chromosome file looks like that, tabbed and with the “chr” removed since ensemble doesn’t include it:

1 248956422

And this is my gtf file:

genome-build GRCh38.p13

genome-version GRCh38

genome-date 2013-12

genome-build-accession NCBI:GCA_000001405.28

genebuild-last-updated 2019-06

1 havana gene 11869 14409 . + . gene_id “ENSG00000223972”; gene_version “5”; gene_name “DDX11L1”; gene_source “havana”; gene_biotype “transcribed_unprocessed_pseudogene”;
1 havana transcript 11869 14409 . + . gene_id “ENSG00000223972”; gene_version “5”; transcript_id “ENST00000456328”; transcript_version “2”; gene_name “DDX11L1”; gene_source “havana”; gene_biotype “transcribed_unprocessed_pseudogene”; transcript_name “DDX11L1-202”; transcript_source “havana”; transcript_biotype “processed_transcript”; tag “basic”; transcript_support_level “1”;

Both cdna and gtf were downloaded from ensemble release 100.

But I am getting this error:

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 190,522
[index] number of k-mers: 110,454,598
[index] number of equivalence classes: 770,729
Warning: could not find chromosomes for 492 transcripts
Warning: 55523 transcripts were defined in GTF file, but not in the index
[quant] running in paired-end mode

I have read about this error for version 46.2 but I am on kallisto 46.1 and the chr problem doesn’t seem to be the case here either since there is only the number both in the chrom sizes and the gtf file

Would appreciate any input.
Many thanks!

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