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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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Figures not being drawn for most chromosomes and missing annotation information #229

Open moldach opened 3 years ago

moldach commented 3 years ago

Despite having a number of events (DEL, BND, DUP, INS) spread out across all chromosome in C. elegans (I, II, III, IV, V, X, MtDNA) I only see illustrations produced:

I'm seeing this for a number of different strains (BAM//VCF' combos) I've runmavis` on.

To Reproduce Steps to reproduce the behavior:

  1. run command:

My directory looks like:

 25M -rw-r----- 1 moldach moldach  25M Oct 27 16:53 ce11.2bit
 33M -rw-r----- 1 moldach moldach  33M Oct 27 16:55 celegans_mavis.json
 98M -rwxr-x--- 1 moldach moldach  98M Oct 27 17:09 c_elegans.PRJNA13758.WS265.genomic.fa
4.0K -rwxr-x--- 1 moldach moldach  181 Oct 27 17:09 c_elegans.PRJNA13758.WS265.genomic.fa.f                                                                                                     ai
4.0K -rw-r----- 1 moldach moldach  519 Oct 28 11:12 mavis.cfg
5.0G -rw-r----- 1 moldach moldach 5.0G Oct 27 17:46 MTG470.sorted.dedupped.bam
304K -rw-r----- 1 moldach moldach 301K Oct 27 19:25 MTG470.sorted.dedupped.bam.bai
124K -rw-r----- 1 moldach moldach 122K Oct 28 11:36 MTG470.vcf
4.0K drwxr-x--- 6 moldach moldach 4.0K Oct 27 19:27 output_dir
  1. See error ...

The output_dir only contains the following images from X chromosome

.
├── build.cfg
├── converted_inputs
│   └── manta.tab
├── maddog_normal_genome
│   ├── annotate
│   │   ├── batch-Gaadu8qALeaQhcBYwwU3GR-1
│   │   │   ├── annotations.fusion-cdna.fa
│   │   │   ├── annotations.tab
│   │   │   ├── drawings
│   │   │   │   ├── mavis_2sDaGWbmHQj7ichDwV5hzB-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_2sDaGWbmHQj7ichDwV5hzB-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_2sDaGWbmHQj7ichDwV5hzB-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_2sDaGWbmHQj7ichDwV5hzB-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_2tZDHqjkZGps5Hb2J4WX6V-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_2tZDHqjkZGps5Hb2J4WX6V-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_2tZDHqjkZGps5Hb2J4WX6V-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_2tZDHqjkZGps5Hb2J4WX6V-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_2wpALnhk3CmmAJ6wxYfj2A-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_2wpALnhk3CmmAJ6wxYfj2A-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_2wpALnhk3CmmAJ6wxYfj2A-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_2wpALnhk3CmmAJ6wxYfj2A-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_2XqEUE6CgeXV37KYkspfAu-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_2XqEUE6CgeXV37KYkspfAu-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_2XqEUE6CgeXV37KYkspfAu-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_2XqEUE6CgeXV37KYkspfAu-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_5MDxQXrh2FPQtSX8SKjP4e-v1-a1-chrX_chrX-NA_b-wrt-2.legend.json
│   │   │   │   ├── mavis_5MDxQXrh2FPQtSX8SKjP4e-v1-a1-chrX_chrX-NA_b-wrt-2.svg
│   │   │   │   ├── mavis_5QMRyxNAGxtmyqhzPcmFsw-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_5QMRyxNAGxtmyqhzPcmFsw-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_5QMRyxNAGxtmyqhzPcmFsw-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_5QMRyxNAGxtmyqhzPcmFsw-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_6LMGhdQKcnRPh3qUYKo4gU-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_6LMGhdQKcnRPh3qUYKo4gU-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_6LMGhdQKcnRPh3qUYKo4gU-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_6LMGhdQKcnRPh3qUYKo4gU-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_6MTV6keJh9SYH6WBDdrpv8-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_6MTV6keJh9SYH6WBDdrpv8-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_6MTV6keJh9SYH6WBDdrpv8-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_6MTV6keJh9SYH6WBDdrpv8-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_6rPsQsjqRj4VZy6r2JZ3Ji-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_6rPsQsjqRj4VZy6r2JZ3Ji-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_6rPsQsjqRj4VZy6r2JZ3Ji-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_6rPsQsjqRj4VZy6r2JZ3Ji-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_7WDA5yzCnt7777ttTaLPzN-v1-a1-chrX_chrX-b-K10B3.5_NA.legend.json
│   │   │   │   ├── mavis_7WDA5yzCnt7777ttTaLPzN-v1-a1-chrX_chrX-b-K10B3.5_NA.svg
│   │   │   │   ├── mavis_863DQ4cBuGEDLH8w9iojm4-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_863DQ4cBuGEDLH8w9iojm4-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_863DQ4cBuGEDLH8w9iojm4-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_863DQ4cBuGEDLH8w9iojm4-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_8JMb9rWaicGbCsaZPSRziP-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_8JMb9rWaicGbCsaZPSRziP-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_8JMb9rWaicGbCsaZPSRziP-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_8JMb9rWaicGbCsaZPSRziP-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_9Fz7vxnCgM7NQmxJWgn9yX-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_9Fz7vxnCgM7NQmxJWgn9yX-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_9Fz7vxnCgM7NQmxJWgn9yX-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_9Fz7vxnCgM7NQmxJWgn9yX-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_9NPTk7v6v64QDSzdB9KufB-v1-a1-chrX_chrX-NA_b-C40C9.4.legend.json
│   │   │   │   ├── mavis_9NPTk7v6v64QDSzdB9KufB-v1-a1-chrX_chrX-NA_b-C40C9.4.svg
│   │   │   │   ├── mavis_adT8fUwHJAerwHrNmhMdVE-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_adT8fUwHJAerwHrNmhMdVE-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_adT8fUwHJAerwHrNmhMdVE-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_adT8fUwHJAerwHrNmhMdVE-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_ar9Z2dCwpBLwqJExdhKwYy-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_ar9Z2dCwpBLwqJExdhKwYy-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_ar9Z2dCwpBLwqJExdhKwYy-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_ar9Z2dCwpBLwqJExdhKwYy-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_BbCoHD7kJcnuXD4QBsEhMf-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_BbCoHD7kJcnuXD4QBsEhMf-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_BbCoHD7kJcnuXD4QBsEhMf-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_BbCoHD7kJcnuXD4QBsEhMf-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_BeWJyDEHzmNHudDSN8z5Lh-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_BeWJyDEHzmNHudDSN8z5Lh-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_BeWJyDEHzmNHudDSN8z5Lh-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_BeWJyDEHzmNHudDSN8z5Lh-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_BHhew8VLLTZZQf4cQDLPGa-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_BHhew8VLLTZZQf4cQDLPGa-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_BHhew8VLLTZZQf4cQDLPGa-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_BHhew8VLLTZZQf4cQDLPGa-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_bqw2TL5pqKrffcunW4t8qx-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_bqw2TL5pqKrffcunW4t8qx-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_bqw2TL5pqKrffcunW4t8qx-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_bqw2TL5pqKrffcunW4t8qx-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_bzbwwAPdKjhzrEVvzY8kum-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_bzbwwAPdKjhzrEVvzY8kum-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_bzbwwAPdKjhzrEVvzY8kum-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_bzbwwAPdKjhzrEVvzY8kum-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_cR7toWFkosHBTLtVdB7FAM-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_cR7toWFkosHBTLtVdB7FAM-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_cR7toWFkosHBTLtVdB7FAM-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_cR7toWFkosHBTLtVdB7FAM-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_DCDnoa4JBRngQQRpSaTEug-v1-a1-chrX_chrX-b-lev-9_b-lev-9.legend.json
│   │   │   │   ├── mavis_DCDnoa4JBRngQQRpSaTEug-v1-a1-chrX_chrX-b-lev-9_b-lev-9.svg
│   │   │   │   ├── mavis_drbPXhcCHRnKgYoQMLbbj8-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_drbPXhcCHRnKgYoQMLbbj8-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_drbPXhcCHRnKgYoQMLbbj8-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_drbPXhcCHRnKgYoQMLbbj8-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_DT52NeB2fHgCNsbtAiQgS7-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_DT52NeB2fHgCNsbtAiQgS7-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_DT52NeB2fHgCNsbtAiQgS7-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_DT52NeB2fHgCNsbtAiQgS7-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_EgG6koz2PXEiCi8KbRL47D-v1-a1-chrX_chrX-NA_b-T26C11.3.legend.json
│   │   │   │   ├── mavis_EgG6koz2PXEiCi8KbRL47D-v1-a1-chrX_chrX-NA_b-T26C11.3.svg
│   │   │   │   ├── mavis_f9bwNkAqqobo5aXVBzkDKS-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_f9bwNkAqqobo5aXVBzkDKS-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_f9bwNkAqqobo5aXVBzkDKS-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_f9bwNkAqqobo5aXVBzkDKS-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_fjK5ojH6kSjTN4eqPUXADr-v1-a1-chrX_chrX-b-nas-39_b-nas-39.legend.json
│   │   │   │   ├── mavis_fjK5ojH6kSjTN4eqPUXADr-v1-a1-chrX_chrX-b-nas-39_b-nas-39.svg
│   │   │   │   ├── mavis_G4o2TtPFijpWULwZACgvyC-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_G4o2TtPFijpWULwZACgvyC-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_G4o2TtPFijpWULwZACgvyC-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_G4o2TtPFijpWULwZACgvyC-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_Gk3MGKUGJRdsNkWCPtuVk8-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_Gk3MGKUGJRdsNkWCPtuVk8-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_Gk3MGKUGJRdsNkWCPtuVk8-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_Gk3MGKUGJRdsNkWCPtuVk8-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_GqqLLAGGN6wNMzBVBU7CT6-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_GqqLLAGGN6wNMzBVBU7CT6-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_GqqLLAGGN6wNMzBVBU7CT6-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_GqqLLAGGN6wNMzBVBU7CT6-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_GyfXSMJCdFybB5WsK6YCnt-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_GyfXSMJCdFybB5WsK6YCnt-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_GyfXSMJCdFybB5WsK6YCnt-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_GyfXSMJCdFybB5WsK6YCnt-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_HAUEs6KDkLeDUyegRAMGUR-v1-a1-chrX_chrX-b-srxa-9_NA.legend.json
│   │   │   │   ├── mavis_HAUEs6KDkLeDUyegRAMGUR-v1-a1-chrX_chrX-b-srxa-9_NA.svg
│   │   │   │   ├── mavis_HAUEs6KDkLeDUyegRAMGUR-v1-a2-chrX_chrX-b-srxa-8_NA.legend.json
│   │   │   │   ├── mavis_HAUEs6KDkLeDUyegRAMGUR-v1-a2-chrX_chrX-b-srxa-8_NA.svg
│   │   │   │   ├── mavis_HmwdK27SqzN3qbY3ph4Lir-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_HmwdK27SqzN3qbY3ph4Lir-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_HmwdK27SqzN3qbY3ph4Lir-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_HmwdK27SqzN3qbY3ph4Lir-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_kASFTibA5yoiiUcBpEqisD-v1-a1-chrX_chrX-b-tsp-8_b-tsp-8.legend.json
│   │   │   │   ├── mavis_kASFTibA5yoiiUcBpEqisD-v1-a1-chrX_chrX-b-tsp-8_b-tsp-8.svg
│   │   │   │   ├── mavis_kifhf3yTMQEPxGGWGjqfeo-v1-a1-chrX_chrX-b-tbc-12_NA.legend.json
│   │   │   │   ├── mavis_kifhf3yTMQEPxGGWGjqfeo-v1-a1-chrX_chrX-b-tbc-12_NA.svg
│   │   │   │   ├── mavis_LfmindF6nzgiTRP4c2qdC2-v2-a1-chrX_chrX-b-lev-9_b-lev-9.legend.json
│   │   │   │   ├── mavis_LfmindF6nzgiTRP4c2qdC2-v2-a1-chrX_chrX-b-lev-9_b-lev-9.svg
│   │   │   │   ├── mavis_Lux2XkajHsYkg6PBtj9e9z-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_Lux2XkajHsYkg6PBtj9e9z-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_Lux2XkajHsYkg6PBtj9e9z-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_Lux2XkajHsYkg6PBtj9e9z-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_MzVha4iwFkerPFfKnnpuac-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_MzVha4iwFkerPFfKnnpuac-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_MzVha4iwFkerPFfKnnpuac-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_MzVha4iwFkerPFfKnnpuac-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_nEWU9tFVdAy6ygaDQXq9vW-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_nEWU9tFVdAy6ygaDQXq9vW-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_nEWU9tFVdAy6ygaDQXq9vW-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_nEWU9tFVdAy6ygaDQXq9vW-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_nQBLDYnVHqFAXEAimYTf8m-v1-a1-chrX_chrX-b-twf-2_b-twf-2.legend.json
│   │   │   │   ├── mavis_nQBLDYnVHqFAXEAimYTf8m-v1-a1-chrX_chrX-b-twf-2_b-twf-2.svg
│   │   │   │   ├── mavis_NtX8keAY2BzksSaGvhorED-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_NtX8keAY2BzksSaGvhorED-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_NtX8keAY2BzksSaGvhorED-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_NtX8keAY2BzksSaGvhorED-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_RDztQYaGz3y8T2NK9gBcM5-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_RDztQYaGz3y8T2NK9gBcM5-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_RDztQYaGz3y8T2NK9gBcM5-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_RDztQYaGz3y8T2NK9gBcM5-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_S6zijee8aWhnfmwHnitL4A-v1-a1-chrX_chrX-b-H03E18.2_b-H03E18.2.legend.json
│   │   │   │   ├── mavis_S6zijee8aWhnfmwHnitL4A-v1-a1-chrX_chrX-b-H03E18.2_b-H03E18.2.svg
│   │   │   │   ├── mavis_SbCVpvZhpnABmxt3JdpwWM-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_SbCVpvZhpnABmxt3JdpwWM-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_SbCVpvZhpnABmxt3JdpwWM-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_SbCVpvZhpnABmxt3JdpwWM-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_Usb26RmtpSWYhekLPbMSey-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_Usb26RmtpSWYhekLPbMSey-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_Usb26RmtpSWYhekLPbMSey-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_Usb26RmtpSWYhekLPbMSey-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_V8PG34muKkxH6bCFZtvhVR-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_V8PG34muKkxH6bCFZtvhVR-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_V8PG34muKkxH6bCFZtvhVR-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_V8PG34muKkxH6bCFZtvhVR-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_VnGFQRPSsPwedNXVvEoDbu-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_VnGFQRPSsPwedNXVvEoDbu-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_VnGFQRPSsPwedNXVvEoDbu-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_VnGFQRPSsPwedNXVvEoDbu-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_XkBF4QJDDjwXv8kfukgZvH-v1-a1-chrX_chrX-b-ins-39_NA.legend.json
│   │   │   │   ├── mavis_XkBF4QJDDjwXv8kfukgZvH-v1-a1-chrX_chrX-b-ins-39_NA.svg
│   │   │   │   ├── mavis_XSrYQipSeZdCFFvWesYKMP-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_XSrYQipSeZdCFFvWesYKMP-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_XSrYQipSeZdCFFvWesYKMP-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_XSrYQipSeZdCFFvWesYKMP-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_ZuCZrGztm5nYrriqUFPKVG-v1-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_ZuCZrGztm5nYrriqUFPKVG-v1-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_ZuCZrGztm5nYrriqUFPKVG-v1-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_ZuCZrGztm5nYrriqUFPKVG-v1-a2-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_ZuCZrGztm5nYrriqUFPKVG-v2-a1-chrX_chrX-NA_NA.legend.json
│   │   │   │   ├── mavis_ZuCZrGztm5nYrriqUFPKVG-v2-a1-chrX_chrX-NA_NA.svg
│   │   │   │   ├── mavis_ZuCZrGztm5nYrriqUFPKVG-v2-a2-chrX_chrX-NA_NA.legend.json
│   │   │   │   └── mavis_ZuCZrGztm5nYrriqUFPKVG-v2-a2-chrX_chrX-NA_NA.svg
│   │   │   ├── job-MA_maddog_batch-Gaadu8qALeaQhcBYwwU3GR-53951928-1.log
│   │   │   └── MAVIS-53951928.COMPLETE
│   │   └── submit.sh
│   ├── cluster
│   │   ├── batch-Gaadu8qALeaQhcBYwwU3GR-1.tab
│   │   ├── cluster_assignment.tab
│   │   ├── clusters.bed
│   │   ├── filtered_pairs.tab
│   │   ├── MAVIS-batch-Gaadu8qALeaQhcBYwwU3GR.COMPLETE
│   │   └── MC_maddog_batch-Gaadu8qALeaQhcBYwwU3GR.log
│   └── validate
│       ├── batch-Gaadu8qALeaQhcBYwwU3GR-1
│       │   ├── contigs.bam
│       │   ├── contigs.blat.log
│       │   ├── contigs.blat_out.pslx
│       │   ├── contigs.fa
│       │   ├── contigs.sorted.bam
│       │   ├── contigs.sorted.bam.bai
│       │   ├── evidence.bed
│       │   ├── igv.batch
│       │   ├── job-MV_maddog_batch-Gaadu8qALeaQhcBYwwU3GR-53951925-1.log
│       │   ├── MAVIS-53951925.COMPLETE
│       │   ├── raw_evidence.bam
│       │   ├── raw_evidence.sorted.bam
│       │   ├── raw_evidence.sorted.bam.bai
│       │   ├── validation-failed.tab
│       │   ├── validation-passed.bed
│       │   └── validation-passed.tab
│       └── submit.sh
├── pairing
│   ├── job-MP_batch-Gaadu8qALeaQhcBYwwU3GR-53951931.log
│   ├── MAVIS-53951931.COMPLETE
│   ├── mavis_paired_maddog.tab
│   └── submit.sh
├── summary
│   ├── filtered_pairs.tab
│   ├── job-MS_batch-Gaadu8qALeaQhcBYwwU3GR-53951939.log
│   ├── MAVIS-53951939.COMPLETE
│   ├── mavis_summary_all_maddog.tab
│   ├── mavis_summary_maddog_non-synonymous_coding_variants.tab
│   └── submit.sh
└── tree.log

10 directories, 225 files

Configuration

[reference]
annotations = celegans_mavis.json
aligner_reference = ce11.2bit
reference_genome = c_elegans.PRJNA13758.WS265.genomic.fa

[schedule]
scheduler = SLURM

[maddog]
library = maddog
protocol = genome
bam_file = MTG470.sorted.dedupped.bam
read_length = 101
median_fragment_size = 354
stdev_fragment_size = 73
strand_specific = False
strand_determining_read = 2
disease_status = normal
inputs = manta

[convert]
assume_no_untemplated = True
manta = convert_tool_output
        MTG470.vcf.gz
        manta
        False

Versions (please complete the following information):

Additional context

Furthermore, it looks like the majority of these figures are missing annotation information (since it says _NA_NA.svg)

annotations no_annotation

creisle commented 3 years ago

@moldach we haven't run celegans ourselves before. It looks like this might have something to do with chromosome names. Could you add the full list the chromosome names as they appear in your reference genome, mavis annotations file, and sample?

moldach commented 3 years ago

Hi @creisle

The names are roman numerals instead of numbers

If it would be helpful I could share published sample for debugging

moldach commented 3 years ago

It took a couple months to figure out downloading the .json annotations a while back (https://github.com/bcgsc/mavis/issues/205) but they look like they completed to me and I can find instances of each of these chromosome in it (with vim).

creisle commented 3 years ago

I was working on the config parts of the code and thought of something we hadn't tried here. There's a parameter in clustering to configure what chromosomes to limit to but you can turn it off. Could you check the cluster logs for limit_to_chr if that is set to the default human chromosomes that may be causing the issue.

moldach commented 3 years ago

Hi @creisle sorry about the delay. I've taken a look in the configuration logs for limit_to_chr and I can confirm that I see human chromosome names here.

There's a parameter in clustering to configure what chromosomes to limit to but you can turn it off.

How do I do this? Is it a parameter I have to supply to mavis config?

creisle commented 3 years ago

No worries, it's a busy time of year for all of us :)

You can either remove it post-config creation or you can set a new default by setting the environment variable pre-generating the config. Setting it to None will default to all chromosomes.

https://mavis.readthedocs.io/en/latest/configuration/settings/#limit_to_chr

export MAVIS_LIMIT_TO_CHR=None

You can see what all the defaults will be/are set to by generating a config file with the --add_defaults flag

mavis config -w default_config.cfg  --add_defaults
cat default_config.cfg

When you do this with the above environment variable set you should see this in the config it generates

limit_to_chr = None