Error running tap2.py on example data: input file does not exist

[rhalperin]

I am trying to run tap2.py on the data in pavfinder/test/transcriptome. I am using the following command:

tap2.py test /results/pavfinder/test/tap --bf test_genes.bf --fq test_1.fastq.gz test_2.fastq.gz --k 32 62 92 --readlen 100 --params test.cfg --remove_fq >pavfinder_test_tap.out 2>pavfinder_test_tap.err

I get the error:

No way to run job: Input file '/results/pavfinder/test/tap/rnabloom_1.4.3/ATXN3/ATXN3.transcripts.fa' does not exist

Here are my log file, stdout, and stderr: log.2022-04-15_15_02_19.txt pavfinder_test_tap.err.txt pavfinder_test_tap.out.txt

Here is what my output directory looks like:

tree /results/pavfinder/test/tap/
/results/pavfinder/test/tap/
├── bbt_2.3.3
│   ├── ATXN3_1.fastq
│   ├── ATXN3_2.fastq
│   ├── CEBPA_1.fastq
│   ├── CEBPA_2.fastq
│   ├── FLT3_1.fastq
│   ├── FLT3_2.fastq
│   ├── FOXP1_1.fastq
│   ├── FOXP1_2.fastq
│   ├── KMT2A_1.fastq
│   ├── KMT2A_2.fastq
│   ├── NPM1_1.fastq
│   ├── NPM1_2.fastq
│   ├── NSD1_1.fastq
│   ├── NSD1_2.fastq
│   ├── NUP98_1.fastq
│   ├── NUP98_2.fastq
│   ├── test_reads.fq
│   └── test_summary.tsv
├── logs
│   ├── log.2022-04-15_14:57:16.txt
│   ├── log.2022-04-15_14:57:22.txt
│   └── log.2022-04-15_15:02:19.txt
├── pv_1.8.0
└── rnabloom_1.4.3
    ├── ATXN3
    ├── CEBPA
    ├── FLT3
    ├── FOXP1
    ├── KMT2A
    ├── NPM1
    ├── NSD1
    └── NUP98

12 directories, 21 files

[kmnip]

It looks like the run failed at the assembly stage. Do you have RNA-Bloom installed?

conda install -c bioconda rnabloom

[rhalperin]

Yes (though I didn't install via conda, I just downloaded the latest release)

rnabloom --version
RNA-Bloom v1.4.3
Ka Ming Nip, Canada's Michael Smith Genome Sciences Centre, BC Cancer
Copyright 2018-present

[rhalperin]

I figured out that I was missing an RNA-Bloom dependency. I fixed that and it works now.