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)
- Program stuck at [IndexRegistry]: Chunking VCF(s) for days HOT 2
- vg alignments not reporting split reads HOT 1
- Mapping paired end reads with vg giraffe: "Falling back on single-end mapping" HOT 9
- Autoindex should parse tabix-indexed monolithic VCFs in parallel
- vg pack error HOT 3
- vg map errors HOT 5
- Genotyping SVs in a minigraph-cactus graph yields many similar alleles in output vcf HOT 1
- How to align both long and paired end short reads using vg HOT 1
- Augmentation failed on one chromosome, but succesfull on other chromosomes HOT 3
- Can VG simulate the third-generations long reads? HOT 5
- Issue with vg map and vg augment for certain inputs. HOT 2
- Merging multiple graph files HOT 4
- short read giraffe alignment crashes most of the time, works on a few random samples - Signal 11 HOT 2
- Running VG deconstruct failed in the gfa generated from PGGB pipline HOT 3
- ERROR vg autoindex :Tag "transcript_id" not found in attributes (line 145). ERROR: Tag "transcript_id" not found in attributes (line 4). ERROR: No transcripts parsed (remember to set feature type "-y" in vg rna or "-f" in vg autoindex) HOT 1
- Error Exceeded Limit of Size on Disk While Running vg index HOT 1
- Mapping paired reads w/ giraffe, no EOF marker, job stalls, exit code 79 HOT 5
- Construct a generation-level pan-genome HOT 5
- Release vg v1.58.0
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