Closed moldach closed 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 toFalse
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?
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?
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
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output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-66/contigs.blat.log
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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
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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
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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
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output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-99/contigs.blat.log
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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
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output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-76/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-76.log
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output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-25/contigs.blat.log
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output_dir/L1522785992-normal_normal_genome/validate/batch-U3NNzG7N6s9jdwsNiSVQmx-78/job-MV_L1522785992-normal_batch-U3NNzG7N6s9jdwsNiSVQmx-53921324-78.log
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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?
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
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?
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
Yep there are no logs from annotating step (see my list of log files above).
Trying to determine why this step was not run.
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/
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
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
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
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_
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
I'm not sure if this is persistent between session or not?
The following returns nothing:
$ source ~/mavis_venv/bin/activate
$ env | grep MAVIS_
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
Following the instructions for the MAVIS (full) tutorial I am surprised to see that there are no images created?