Hello Biostars community,

We would like to ask whether anyone is able to create an index using hisat2-build with --ss (splice sites) and --exon on the below refseq files. If you have had issues related to this in the past, would also be useful to hear any advice/lessons learned.

Current pain point:

• hisat2-build stalls at generation 4 for 20 hours (log below) despite indication from top, that program is running.
• GCF_000001405.40_GRCh38.p14_genomic.gtf.gz build completes successfully without --ss and --exon.
• In the past, we have successfully buit an index, using these settings on the Gencode v42/41/39 comprehensive fasta and gtf files (with --exon and --ss).

Setup: hisat2 version hisat2 2.2.1 (latest)

version refseq -GCF_000001405.40_GRCh38.p14_genomic.fna.gz 2024-08-27 09:57 928M -GCF_000001405.40_GRCh38.p14_genomic.gtf.gz 2024-08-27 09:57 54M

machine stats Local VM: 20 Core CPU , 256 RAM , 1.6 TB hd space,

Extract exon: hisat2_extract_exons.py GCF_000001405.40_GRCh38.p14_genomic.sorted.gtf > Original_refseq1405.40_extractexon

Extract splice: hisat2_extract_splice_sites.py GCF_000001405.40_GRCh38.p14_genomic.sorted.gtf > Original_refseq1405.40_extractsplice

hisat2-build: hisat2-build -p 4 --exon Original_refseq1405.40_extractexon --ss Original_refseq1405.40_extractsplice GCF_000001405.40_GRCh38.p14_genomic.fna HISAT_RefSeq1405_40_Full_Index_SS_Exon

(also tested without any thread assignment (-p))

Thanks in advance, Chris

Log out: 

Settings:
  Output files: "HISAT_RefSeq1405_40_Full_Index/HISAT_RefSeq1405_40_Full_Index_SS_Exon.*.ht2"
  Line rate: 7 (line is 128 bytes)
  Lines per side: 1 (side is 128 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Local offset rate: 3 (one in 8)
  Local fTable chars: 6
  Local sequence length: 57344
  Local sequence overlap between two consecutive indexes: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  GCF_000001405.40_GRCh38.p14_genomic.fna
Reading reference sizes
  Time reading reference sizes: 00:00:42
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:13
  Time to read SNPs and splice sites: 00:00:02
Generation 0 (3137151402 -> 3137151402 nodes, 0 ranks)
COUNTED NEW NODES: 8
COUNTED TEMP NODES: 0
RESIZED NODES: 20
RESIZED NODES: 0
MADE NEW NODES: 22
Generation 1 (3137468813 -> 3137468813 nodes, 0 ranks)
COUNTED NEW NODES: 6
COUNTED TEMP NODES: 0
RESIZED NODES: 19
RESIZED NODES: 0
MADE NEW NODES: 23
Generation 2 (3138104089 -> 3138104089 nodes, 0 ranks)
COUNTED NEW NODES: 6
COUNTED TEMP NODES: 0
RESIZED NODES: 20
RESIZED NODES: 0
MADE NEW NODES: 23
Generation 3 (3139375392 -> 3139375392 nodes, 0 ranks)
BUILT FROM_INDEX: 17
COUNTED NEW NODES: 6
COUNTED TEMP NODES: 0
RESIZED NODES: 20
RESIZED NODES: 0
MADE NEW NODES: 24
RESIZE NODES: 68
COUNT NUMBER IN EACH BIN: 14
FINISHED FIRST ROUND: 26
26 789568741
103 841602280
67 786479349
170 724271090
FINISHED RECURSIVE SORTS: 87
SORT NODES: 127
MERGE, UPDATE RANK: 69
Generation 4 (3141921460 -> 3141356782 nodes, 1139244126 ranks)
ALLOCATE FROM_TABLE: 32
COUNT NUMBER IN EACH BIN: 13
FINISHED FIRST ROUND: 36
94 789748680
94 789476690
93 781444256
93 780687156
FINISHED RECURSIVE SORTS: 71
BUILD TABLE: 120
BUILD INDEX: 18
82 nodes, 1139244126 ranks)
ALLOCATE FROM_TABLE: 32
COUNT NUMBER IN EACH BIN: 13
FINISHED FIRST ROUND: 36