Roberto Vera Alvarez

Hi @mr-c and @tetron, is anyone taking care of this issue? This is a serious bug if is using cwltool with the `parallel` and `beta-conda-dependencies` options at the same time.

Hi Michael, Here is the command line I used to generate the error: `cwltool 3.0.20210124104916` Command: ``` cwltool --debug --no-container --beta-conda-dependencies --beta-dependencies-directory ./cwltool_deps --parallel --on-error continue --rm-tmpdir --tmp-outdir-prefix=./tmp/ --tmpdir-prefix=./tmp/ /panfs/pan1.be-md.ncbi.nlm.nih.gov/alt_splicing/cookiecutter/Drosophila_Lol_Mutant/bin/cwl/workflows/sra/download_quality_control.cwl...

Hi, This is the normal way TPMCalculator quantify RNA-Seq abundance on copies for a same gene. If you look at the output, the third column is the starting coordinate of...

We identify the copies using the genomic coordinates. If the transcripts of a same gene are in different genomic region and they don't overlap we mark that as a copy...

Hi, The GTF format are 1-base, it mean that the positions start at 1 but BAM files are 0-base. TPMCalculator move the feature coordinates to 0-base and print then in...

Hi, TPMCalculator creates a gene model by overlapping the exons of all isoforms of a gene. The -c option set the minimum size for creating an intron when overlapping multiple...

That feature will be include in the next release.

The model to describe the genomic features used for a gene is created from the GTF provided by the user. TPMCalculator performs two transformations which are executed on the genomic...

Hi, could you, please share a few reads from your BAM file and the GTF?

Hi, Don't use the -d option and run one TPMCalculator for BAM file using the -b option. The message: "Chromosome with name: GL000008.2 does not exist" is saying that you...