error prepping reference (cannot find abundance.tsv file) for kallisto

[Jane]

Hi,

I am trying to run abundance estimation using kallisto using the Trinity protocol. I was trying to prep the reference, after which I am planning on running abundance estimation for each of my samples at a time.

I was running this:
Trinity/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --est_method kallisto --trinity_mode --prep_reference --output_dir kallisto

But I get the following error about not having an abundance.tsv file:

CMD: Trinity/util/support_scripts/kallisto_trans_to_gene_results.pl out/abundance.tsv kallisto/Trinity.fasta.gene_trans_map > out/abundance.tsv.genes

bash: out/abundance.tsv.genes: No such file or directory

Error, cmd: Trinity/util/support_scripts/kallisto_trans_to_gene_results.pl out/abundance.tsv kallisto/Trinity.fasta.gene_trans_map > out/abundance.tsv.genes died with ret: 256 at Trinity/util/align_and_estimate_abundance.pl line 714.

Does anyone have any suggestions about how I can fix this? For reference, this error did not happen when I ran RSEM or eXpress using the same script with assembly mapping options.

Thanks,

Jane

[Jane]

Ok, so for some reason it really hated running "Just prepare the reference for alignment and abundance estimation"

When I run "prep the reference and run the alignment/estimation" with the sample files it now works.