LiftOver stuck after starting

[JavierMenRev]

I am using the following command to LiftOver a VCF file from hg19 to hg38:

java -Xmx32g -jar ${PPATH}/picard_2.20.1/picard.jar LiftoverVcf
I=chr15_hg19.vcf
O=test.vcf
CHAIN=hg19ToHg38.over.chain
REJECT=test_hg38_reject.vcf
R=GRCh38_full_analysis_set_plus_decoy_hla.fa
TMP_DIR=${SP}

The VCF file has over 40M sites (it includes monomorphic REF/REF genotypes) for a single individual

This is basically the header of the log file:

[Sat Apr 02 16:02:54 CEST 2022] Executing as jmendoza@maestro-1091 on Linux 4.18.0-193.70.1.el8_2.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 13.0.2+8; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.20.1-SNAPSHOT
INFO 2022-04-02 16:02:54 LiftoverVcf Loading up the target reference genome.
INFO 2022-04-02 16:03:10 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.)

It's been stuck like that for more than 24 hours.

The strange this is that I am running the exact same command for the same individual, but for a larger chromosome (e.g. chr3, chr4 and chr5) and all these runs have finished.

For example the header of the log file of chr3 looks like this:

INFO 2022-04-02 16:07:04 LiftoverVcf Loading up the target reference genome.
INFO 2022-04-02 16:07:21 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.)
INFO 2022-04-02 16:07:32 LiftoverVcf read 1,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 10s. Last read position: chr3:1,758,639
INFO 2022-04-02 16:07:41 LiftoverVcf read 2,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 9s. Last read position: chr3:3,363,024
INFO 2022-04-02 16:07:48 LiftoverVcf read 3,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 6s. Last read position: chr3:5,060,870
.
.
.

And finished in ~20 min.

I am not sure why it would take longer for chr15.

Thank you,