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bcgsc / mavis

Merging, Annotation, Validation, and Illustration of Structural variants
http://mavis.bcgsc.ca
GNU General Public License v3.0
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No drawings in example output #228

Closed moldach closed 3 years ago

moldach commented 3 years ago

Following the instructions for the MAVIS (full) tutorial I am surprised to see that there are no images created?

find output_dir -name "*.svg" returns nothing

moldach commented 3 years ago

Images are only created when first doing:

export MAVIS_DRAW_FUSIONS_ONLY=False

Then there are > 8000 figures drawn.

(mavis_venv) [moldach@cedar1 output_dir2]$ find . -name "*.svg" | wc -l
8080

According to the Illustrations documentation:

These are diagrams produced during the annotate step. These represent the putative fusion events of a single breakpoint pair. If the draw_fusions_only flag is set to False then all events will produce a diagram, even anti-sense fusions.

What does this mean? Does this mean that all of these SVs are in Non-coding regions?

calchoo commented 3 years ago

Hi @moldach, I ran the tutorial data again as was able to generate images without adding the MAVIS_DRAW_FUSIONS_ONLY=False option.

We're you using any other custom configurations? Could you post some of the logs?

moldach commented 3 years ago

There's quite a few logs (219) are there any in particular you're looking for? Might have to share on dropbox 😅

(mavis_venv) [moldach@cedar1 foo]$ find output_dir -name "*.log" | wc -l
219

(mavis_venv) [moldach@cedar1 foo]$ find output_dir -name "*.log"
output_dir/L1522785992-trans_diseased_transcriptome/cluster/MC_L1522785992-trans_batch-U3NNzG7N6s9jdwsNiSVQmx.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-57/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-57/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-57.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-30/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-30/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-30.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-29/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-29/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-29.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-107/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-107/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-107.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-86/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-86/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-86.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-88/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-88/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-88.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-45/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-45/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-45.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-18/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-18/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-18.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-44/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-44/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-44.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-22/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-22/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-22.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-41/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-41/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-41.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-14/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-14/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-14.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-58/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-58/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-58.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-12/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-12/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-12.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-3/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-3/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-3.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-85/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-85/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-85.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-80/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-80/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-80.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-19/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-19/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-19.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-66/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-66/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-66.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-70/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-70/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-70.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-31/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-31/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-31.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-53/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-53/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-53.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-1/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-1/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-1.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-4/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-4/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-4.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-48/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-48/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-48.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-47/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-47/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-47.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-49/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-49/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-49.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-20/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-20/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-20.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-108/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-108/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-108.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-59/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-59/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-59.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-99/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-99/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-99.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-71/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-71/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-71.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-10/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-10/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-10.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-67/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-67/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-67.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-76/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-76/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-76.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-42/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-42/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-42.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-28/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-28/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-28.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-40/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-40/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-40.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-73/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-73/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-73.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-25/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-25/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-25.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-78/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-78/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-78.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-56/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-56/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-56.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-103/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-103.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-103/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-37/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-37/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-37.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-13/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-13/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-13.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-81/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-81/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-81.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-50/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-50/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-50.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-61/contigs.blat.log
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output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-97/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-97/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-97.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-95/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-95/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-95.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-94/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-94/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-94.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-7/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-7/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-7.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-102/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-102.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-102/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-101/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-101/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-101.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-46/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-46/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-46.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-79/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-79/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-79.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-84/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-84/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-84.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-89/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-89/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-89.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-68/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-68/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-68.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-75/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-75/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-75.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-100/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-100/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-100.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-32/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-32/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-32.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-98/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-98/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-98.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-15/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-15/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-15.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-34/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-34/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-34.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-52/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-52/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-52.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-104/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-104/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-104.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-33/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-33/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-33.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-54/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-54/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-54.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-93/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-93/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-93.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-92/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-92/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-92.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-26/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-26/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-26.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-83/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-83/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-83.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-38/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-38/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-38.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-51/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-51/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-51.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-96/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-96/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-96.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-77/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-77/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-77.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-27/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-27/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-27.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-2/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-2/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-2.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-16/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-16/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-16.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-8/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-8/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-8.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-21/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-21/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-21.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-5/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-5/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-5.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-106/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-106/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-106.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-62/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-62/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-62.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-36/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-36/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-36.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-24/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-24/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-24.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-105/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-105/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-105.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-35/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-35/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-35.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-74/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-74/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-74.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-9/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-9.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-9/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-11/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-11/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-11.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-63/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-63/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-63.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-82/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-82/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-82.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-91/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-91/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-91.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-60/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-60/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-60.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-90/contigs.blat.log
output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-90/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-90.log
output_dir/L1522785992-normal_normal_genome/cluster/MC_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx.log
output_dir/L1522785992-tumour_diseased_genome/cluster/MC_L1522785992-tumour_batch-U3NNzG7N6s9jdwsNiSVQmx.log

Looking for any in particular?

calchoo commented 3 years ago

I'm looking for the settings listed in one of the headers of the annotate log files

e.g

~> head -n 45 annotate/batch-YMHGRQiF9UJj7mhfdGHzSo-83/job-MA_L1522785992-tumour_batch-YMHGRQiF9UJj7mhfdGHzSo-83-nGXigZargpFDiUbh7T6i5s.log
                      MAVIS: 2.2.7
                      hostname: gphost01.bcgsc.ca
[2020-11-05 14:54:08] arguments
                        annotation_filters = 'choose_more_annotated,choose_transcripts_by_priority'
                        annotations = ['/projects/trans_scratch/validations/workspace/cchoo/mavis/test/reference_inputs/ensembl69_hg19_annotations.json']
                        breakpoint_color = '#000000'
                        command = 'annotate'
                        domain_color = '#ccccb3'
                        domain_mismatch_color = '#b2182b'
                        domain_name_regex_filter = '^PF\\d+$'
                        domain_scaffold_color = '#000000'
                        draw_fusions_only = True
                        draw_non_synonymous_cdna_only = True
                        drawing_width_iter_increase = 500
                        exon_min_focus_size = 10
                        gene1_color = '#657e91'
                        gene1_color_selected = '#518dc5'
                        gene2_color = '#325556'
                        gene2_color_selected = '#4c9677'
                        inputs = ['/projects/trans_scratch/validations/workspace/cchoo/mavis/test/output_dir2/L1522785992-tumour_diseased_genome/validate/batch-YMHGRQiF9UJj7mhfdGHzSo-83/validation-passed.tab']
                        label_color = '#000000'
                        library = 'L1522785992-tumour'
                        log = '/projects/trans_scratch/validations/workspace/cchoo/mavis/test/output_dir2/L1522785992-tumour_diseased_genome/annotate/batch-YMHGRQiF9UJj7mhfdGHzSo-83/job-MA_L1522785992-tumour_batch-YMHGRQiF9UJj7mhfdGHzSo-83-nGXigZargpFDiUbh7T6i5s.log'
                        log_level = 'INFO'
                        mask_fill = '#ffffff'
                        mask_opacity = 0.7
                        masking = ['/projects/trans_scratch/validations/workspace/cchoo/mavis/test/reference_inputs/hg19_masking.tab']
                        max_drawing_retries = 5
                        max_orf_cap = 3
                        max_proximity = 5000
                        min_domain_mapping_match = 0.9
                        min_orf_size = 300
                        novel_exon_color = '#5D3F6A'
                        output = '/projects/trans_scratch/validations/workspace/cchoo/mavis/test/output_dir2/L1522785992-tumour_diseased_genome/annotate/batch-YMHGRQiF9UJj7mhfdGHzSo-83'
                        protocol = 'genome'
                        reference_genome = ['/projects/trans_scratch/validations/workspace/cchoo/mavis/test/reference_inputs/hg19.fa']
                        scaffold_color = '#000000'
                        splice_color = '#000000'
                        template_metadata = ['/projects/trans_scratch/validations/workspace/cchoo/mavis/test/reference_inputs/cytoBand.txt']
                        width = 1000
                      cached content: ['/projects/trans_scratch/validations/workspace/cchoo/mavis/test/reference_inputs/cytoBand.txt']
                      creating output directory: '/projects/trans_scratch/validations/workspace/cchoo/mavis/test/output_dir2/L1522785992-tumour_diseased_genome/annotate/batch-YMHGRQiF9UJj7mhfdGHzSo-83/drawings'
                      loading: /projects/trans_scratch/validations/workspace/cchoo/mavis/test/output_dir2/L1522785992-tumour_diseased_genome/validate/batch-YMHGRQiF9UJj7mhfdGHzSo-83/validation-passed.tab
                      loaded 29 breakpoint pairs
                      read 29 breakpoint pairs
moldach commented 3 years ago

Of all those 219 log files I provided there are no log files in the /annotations directory.

Which of those logs I listed above will help you assess why?

creisle commented 3 years ago

There should be logs in the annotate directory. Following the example @calchoo posted above they would look something like this

annotate/batch-YMHGRQiF9UJj7mhfdGHzSo-83/job-MA_L1522785992-tumour_batch-YMHGRQiF9UJj7mhfdGHzSo-83-nGXigZargpFDiUbh7T6i5s.log

Does your output have anything like that? if not it may indicate the annotate step was not run or stopped for some reason which might explain the lack of figures

moldach commented 3 years ago

Yep there are no logs from annotating step (see my list of log files above).

Trying to determine why this step was not run.

Installation

module load python/3.8.2
python -m venv ~/bin/mavis_venv
source ~/bin/mavis_venv/bin/activate
pip install --upgrade pip setuptools
pip install mavis

mkdir MAVIS-TUTORIAL; cd MAVIS-TUTORIAL
git clone https://github.com/bcgsc/mavis.git
mv mavis/tests .
rm -r mavis/

Getting MAVIS tutorial data

wget http://www.bcgsc.ca/downloads/mavis/tutorial_data.tar.gz
tar -xvzf tutorial_data.tar.gz
wget https://raw.githubusercontent.com/bcgsc/mavis/master/tools/get_hg19_reference_files.sh
bash get_hg19_reference_files.sh
source reference_inputs/hg19_env.sh

Make Config

salloc --time=3:0:0 --mem=20000
source ~/bin/mavis_venv/bin/activate

mavis config \
    --library L1522785992-normal genome normal False tutorial_data/L1522785992_normal.sorted.bam \
    --library L1522785992-tumour genome diseased False tutorial_data/L1522785992_tumour.sorted.bam \
    --library L1522785992-trans transcriptome diseased True tutorial_data/L1522785992_trans.sorted.bam \
    --convert breakdancer tutorial_data/breakdancer-1.4.5/*txt breakdancer \
    --convert breakseq tutorial_data/breakseq-2.2/breakseq.vcf.gz breakseq \
    --convert chimerascan tutorial_data/chimerascan-0.4.5/chimeras.bedpe chimerascan \
    --convert defuse tutorial_data/defuse-0.6.2/results.classify.tsv defuse \
    --convert manta tutorial_data/manta-1.0.0/diploidSV.vcf.gz tutorial_data/manta-1.0.0/somaticSV.vcf manta \
    --assign L1522785992-trans chimerascan defuse \
    --assign L1522785992-tumour breakdancer breakseq manta  \
    --assign L1522785992-normal breakdancer breakseq manta \
    -w mavis.cfg

Setting up

mavis setup mavis.cfg -o output_dir/
mavis schedule -o output_dir --submit

freeze

(mavis_venv) [moldach@cedar1 mavis-test]$ pip freeze
-f /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/nix/avx2
-f /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/nix/generic
-f /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic
biopython==1.77
braceexpand==0.1.2
colour==0.1.5
decorator==4.4.2
Distance==0.1.3
mavis==2.2.7
networkx==1.11
numpy==1.19.1
pysam==0.15.2
PyVCF==0.6.8
Shapely==1.7.0
shortuuid==1.0.1
svgwrite==1.4
creisle commented 3 years ago

I don't see anything obvious from the commands, could you paste the content of the generated config? as well as check if you have any mavis environment variables set? (see command below)

env | grep MAVIS_
moldach commented 3 years ago

Contents of mavis.cfg

[reference]
template_metadata = /scratch/moldach/MAVIS-TUTORIAL/reference_inputs/cytoBand.txt
masking = /scratch/moldach/MAVIS-TUTORIAL/reference_inputs/hg19_masking.tab
annotations = /scratch/moldach/MAVIS-TUTORIAL/reference_inputs/ensembl69_hg19_annotations.json
aligner_reference = /scratch/moldach/MAVIS-TUTORIAL/reference_inputs/hg19.2bit
dgv_annotation = /scratch/moldach/MAVIS-TUTORIAL/reference_inputs/dgv_hg19_variants.tab
reference_genome = /scratch/moldach/MAVIS-TUTORIAL/reference_inputs/hg19.fa

[L1522785992-normal]
library = L1522785992-normal
protocol = genome
bam_file = tutorial_data/L1522785992_normal.sorted.bam
read_length = 150
median_fragment_size = 431
stdev_fragment_size = 98
strand_specific = False
strand_determining_read = 2
disease_status = normal
inputs = breakdancer
    manta
    breakseq

[L1522785992-tumour]
library = L1522785992-tumour
protocol = genome
bam_file = tutorial_data/L1522785992_tumour.sorted.bam
read_length = 150
median_fragment_size = 433
stdev_fragment_size = 92
strand_specific = False
strand_determining_read = 2
disease_status = diseased
inputs = breakdancer
    manta
    breakseq

[L1522785992-trans]
library = L1522785992-trans
protocol = transcriptome
bam_file = tutorial_data/L1522785992_trans.sorted.bam
read_length = 75
median_fragment_size = 196
stdev_fragment_size = 51
strand_specific = True
strand_determining_read = 2
disease_status = diseased
inputs = chimerascan
    defuse

[convert]
assume_no_untemplated = True
breakdancer = convert_tool_output
    tutorial_data/breakdancer-1.4.5/chr10.output.txt
    tutorial_data/breakdancer-1.4.5/chr11.output.txt
    tutorial_data/breakdancer-1.4.5/chr12.output.txt
    tutorial_data/breakdancer-1.4.5/chr13.output.txt
    tutorial_data/breakdancer-1.4.5/chr14.output.txt
    tutorial_data/breakdancer-1.4.5/chr15.output.txt
    tutorial_data/breakdancer-1.4.5/chr16.output.txt
    tutorial_data/breakdancer-1.4.5/chr17.output.txt
    tutorial_data/breakdancer-1.4.5/chr18.output.txt
    tutorial_data/breakdancer-1.4.5/chr19.output.txt
    tutorial_data/breakdancer-1.4.5/chr1.output.txt
    tutorial_data/breakdancer-1.4.5/chr20.output.txt
    tutorial_data/breakdancer-1.4.5/chr21.output.txt
    tutorial_data/breakdancer-1.4.5/chr22.output.txt
    tutorial_data/breakdancer-1.4.5/chr2.output.txt
    tutorial_data/breakdancer-1.4.5/chr3.output.txt
    tutorial_data/breakdancer-1.4.5/chr4.output.txt
    tutorial_data/breakdancer-1.4.5/chr5.output.txt
    tutorial_data/breakdancer-1.4.5/chr6.output.txt
    tutorial_data/breakdancer-1.4.5/chr7.output.txt
    tutorial_data/breakdancer-1.4.5/chr8.output.txt
    tutorial_data/breakdancer-1.4.5/chr9.output.txt
    tutorial_data/breakdancer-1.4.5/chrX.output.txt
    tutorial_data/breakdancer-1.4.5/chrY.output.txt
    tutorial_data/breakdancer-1.4.5/translocations.output.txt
    breakdancer
    False
breakseq = convert_tool_output
    tutorial_data/breakseq-2.2/breakseq.vcf.gz
    breakseq
    False
chimerascan = convert_tool_output
    tutorial_data/chimerascan-0.4.5/chimeras.bedpe
    chimerascan
    False
defuse = convert_tool_output
    tutorial_data/defuse-0.6.2/results.classify.tsv
    defuse
    False
manta = convert_tool_output
    tutorial_data/manta-1.0.0/diploidSV.vcf.gz
    tutorial_data/manta-1.0.0/somaticSV.vcf
    manta
    False

Mavis environment variables set?

I'm not sure if this is persistent between session or not?

The following returns nothing:

$ source ~/mavis_venv/bin/activate
$ env | grep MAVIS_
moldach commented 3 years ago

Similar to issue #232 this seems to have been caused by blat not being available in the path (I was trying to use bwa-mem before but blat results should be... better?).

Using module load blat prior to building the mavis.cfg seems to have solved this problem as I now see many figures from the full_tutorial.

$ find output_dir -name "*.svg" | wc -l
100