Unrecoverable error in GCSA2 indexing

[ld9866]

Dear developer:
I used 29 genomes to get the vcf file using the Minigraph-Cactus pipeline, and now I want to do some pan-transcriptome analysis, so I need to convert the required file.

there is still enough storage, but the task automatically terminates after running for one day, I would like to ask how to solve this situation?

l only not obtain the sample.trans.spliced.gcsa and sample.trans.spliced.gcsa.lcp, other files are ok.

Best
Dong

Code:
vg autoindex --threads 32 --workflow mpmap --workflow rpvg --prefix sample.trans --ref-fasta reference.fa --vcf sample.result.vcf.gz --tx-gff Duroc.111.chr1-18.gtf --tmp-dir /home/test/nvmedata2/02.Pantrans/TMP -M 850G
erro:
warning:[vg::Constructor] Skipping duplicate variant with hash c5757e8eca1e42a9bafd6bf1aed0bacad2826367 at 1:274146418
[IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input.
[IndexRegistry]: Merging contig GBWTs.
[IndexRegistry]: Stripping allele paths from spliced VG.
[IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG.
[IndexRegistry]: Merging contig GBWTs.
[IndexRegistry]: Joining transcript origin table.
[IndexRegistry]: Constructing spliced XG graph from spliced VG graph.
[IndexRegistry]: Constructing distance index for a spliced graph.
[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding.
[IndexRegistry]: Constructing GCSA/LCP indexes.
PathGraphBuilder::write(): Memory use of file 0 of kmer paths (850.002 GB) exceeds memory limit (850 GB)
PathGraphBuilder::write(): Memory use of file 0 of kmer paths (850.045 GB) exceeds memory limit (850 GB)
[IndexRegistry]: Exceeded disk or memory use limit while performing k-mer doubling steps. Rewinding to pruning step with more aggressive pruning to simplify the graph.
[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding.
[IndexRegistry]: Constructing GCSA/LCP indexes.
PathGraphBuilder::write(): Memory use of file 0 of kmer paths (850.017 GB) exceeds memory limit (850 GB)
PathGraphBuilder::write(): Memory use of file 0 of kmer paths (850.06 GB) exceeds memory limit (850 GB)
[IndexRegistry]: Exceeded disk or memory use limit while performing k-mer doubling steps. Rewinding to pruning step with more aggressive pruning to simplify the graph.
[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding.
[IndexRegistry]: Constructing GCSA/LCP indexes.
PathGraphBuilder::write(): Memory use of file 0 of kmer paths (850.039 GB) exceeds memory limit (850 GB)
PathGraphBuilder::write(): Memory use of file 0 of kmer paths (850.082 GB) exceeds memory limit (850 GB)
[IndexRegistry]: Exceeded disk or memory use limit while performing k-mer doubling steps. Rewinding to pruning step with more aggressive pruning to simplify the graph.
[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding.
[IndexRegistry]: Constructing GCSA/LCP indexes.
DiskIO::write(): Write failed
DiskIO::write(): You may have run out of temporary disk space at /home/test/nvmedata2/02.Pantrans/TMP
[IndexRegistry]: Unrecoverable error in GCSA2 indexing.

[adamnovak]

Probably we should have been talking about the problem here, but it looks like we're actually working in #4404 instead.