Comments (9)
I'd suggest not using vg augment
-- just call the SVs directly on your graph.
Others have had issues where GraphAligner does not write mapping qualities (you can check your GAM with vg view -a
). In this case, any MAPQ filter (vg pack -Q 5
or in your case vg augment -Q 5
) will filter all the reads leading to no calls. Try
vg convert -g whole_genome.gfa -p -t 32 > output_WG.pg
vg snarls -t 32 output_WG.pg > mapped_LW_aug.snarls
vg pack -t 32 -x output_WG.pg -g mapped_LW.gam -o mapped_LW.pack
vg call output_WG.pg -t 32 -r mapped_LW.snarls -k mapped_LW.pack > mapped_LW_snarls.vcf
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after running this code for over 4 hours it is still an empty file. the first couple steps took only a fraction, but the vcf file stays empty
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I was also wondering how the vcf file is generated. Does the entire vcf have to be loaded into memory and is then pasted into the output file, or is it procedurally generated in the output?
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It outputs the VCF all at once at the end. vg call
can be very slow on some complex graphs. You can often manage this by using -C
to limit the size of alt alleles to search for in the graph.
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Do you know what would be a good cutoff value be when looking in a mammalian genome?
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And what timeframe should I keep in mind for producing the VCF file, my gam file is 27.7 GB, the reads are 38.3 GB, my VG graph is 6.06 GB and contains 52.4 million nodes, 71.9 million edges and a total length of 2.7 billion.
Thank!
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There's a --progress
option that may help you judge where it is. Otherwise, the running time is extremely dependent on the graph. If you have many reference paths, using -p/-S
to select a reference can help. If you have many haplotypes in general in your graph, you can convert it to gbz
with vg gbwt
and run call with -z
to only explore these haplotypes (speeding up the search)
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Unfortunately the --progress option is not available for me in vg call, but I will try to run with gbz and see how that goes
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When trying to run with a gbz file, I encounter the following error, what could cause this? I am running the following code now:
vg gbwt -G /minigraph_cactus/output_WG/output_WG.gfa -o output_WG.gbwt -d temp -p
vg gbwt -G /minigraph_cactus/output_WG/output_WG.gfa --graph-name output_WG.gbz --gbz-format -p
vg snarls -t 32 output_WG.gbz > mapped_LW.snarls
vg pack -t 32 -x output_WG.gbz -g graphaligner/mapped_LW.gam -o mapped_LW.pack
vg call output_WG.gbz -z -t 32 -r mapped_LW.snarls -k mapped_LW.pack -C 100000 > mapped_C100000_LW_snarls_git.vcf
vg: /private/groups/patenlab/jeizenga/GitHub/vg/include/sdsl/int_vector.hpp:1391: sdsl::int_vector< >::reference sdsl::int_vector< >::operator[](const size_type&) [with unsigned char t_width = 0; sdsl::int_vector< >::reference = sdsl::int_vector_reference<sdsl::int_vector<0> >; sdsl::int_vector< >::size_type = long unsigned int]: Assertion `idx < this->size()' failed.
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Crash report for vg v1.55.0 "Bernolda"
Stack trace (most recent call last) in thread 872463:
#14 Object "", at 0xffffffffffffffff, in
#13 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x2160633, in __clone
#12 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x20b9d4a, in start_thread
#11 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x205c5dd, in gomp_thread_start
#10 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x205ef27, in gomp_team_barrier_wait_end
#9 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x205682a, in gomp_barrier_handle_tasks
#8 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0xdbc505, in void vg::io::for_each_parallel_implvg::Alignment(std::istream&, std::function<void (vg::Alignment&, vg::Alignment&)> const&, std::function<void (vg::Alignment&)> const&, std::function<bool ()> const&, unsigned long) [clone ._omp_fn.1]
#7 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x1272b8a, in vg::Packer::add(vg::Alignment const&, int, int, int)
#6 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x126a338, in vg::Packer::increment_coverage(unsigned long)
#5 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x1264a71, in sdsl::int_vector<(unsigned char)0>::operator[](unsigned long const&) [clone .isra.0]
#4 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x2088545, in __assert_fail
#3 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x5e6053, in __assert_fail_base.cold
#2 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x5e612b, in abort
#1 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x208eb55, in raise
#0 Object "/lustre/nobackup/TOPIGS/shared/swen/cactus-bin-v2.8.0/bin/vg", at 0x20bb56c, in __pthread_kill
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Please include this entire error log in your bug report!
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Related Issues (20)
- Bump necessary magic numbers for long-read index types HOT 1
- vg autoindex --workflow mpmap HOT 1
- GAF nodes do not correspond to VCF nodes HOT 3
- Fastq analysis in euka HOT 2
- Protobuf errors mapping HOT 4
- vg augment crashes in combination with giraffe .gam outputs HOT 5
- when i do the code :vg stats -a var1.gam > var1.stats ,show me a bug HOT 2
- vg surject and pack fail on GraphAligner produced .gam HOT 4
- About the usage of vg deconstruct HOT 5
- Right method to annotate genes on pangenome graph HOT 1
- vg call report missing allele HOT 2
- vg call error HOT 2
- How do different methods affect precision? HOT 4
- Giraffe alignment is very slow and produces warning[vg::Watchdog] messages unless rescue is disabled HOT 13
- Giraffe needs to better deal with systems where multiple processes opening the distance index causes slowdowns
- Any option like BWA MEM '-C'? HOT 1
- vg convert failes while converting gbz to xg with signal 6 error HOT 8
- Release vg v1.60.0
- `vg convert --vg-algorithm` loses start coordinates of paths in its W lines HOT 3
- The Amazing Uninjectable SAM HOT 1
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