There could be a mismatch between chromosome names.

Can you show the first 10 lines of hg19.gtf and hg19_chromsizes.txt as well as the names of the chromosomes you see in IGV (these are taken from the FASTA file provided for the genome). If the names do not match IGV will not display anything.

My guess is that the GTF file has chr1 whereas IGV is using 1, etc. The solution is to fix one of those names.

Since we don't have access to your data, here are a possible check sums

I am assuming hg19.idx is the index generated using transcriptome sequences and not the reference genome since kallisto aligns reads against transcriptome (not genome).

There are 2 possible bam options, --pseudobam or --genomebam. Former is bam against transcriptome while later against genome.

If former you want to visualize in igv, then make sure bam index file (bai) is available in the same directory as bam. e.g. pseudoalignments.bam and pseudoalignments.bam.bai

If later you want, then u need gtf and chromosome length file, which in the command you have already given. So please check whether chromosome names in gtf file (-gtf) and chromosome file (-chromosome) matches.

Manual says "For a larger transcriptome we recommend downloading the GTF file from the same release and data source as the FASTA file used to construct the index." so check whether the chromosome information in hg19.idx files and gtf matches.

Hope you find solution