Are you using the latest version of samtools and HTSlib? If not, please specify.

(run samtools --version)

I am using samtools 1.11 (htslib 1.11)

Please describe your environment.

• OS (run uname -sr on Linux/Mac OS or wmic os get Caption, Version on Windows)
• machine architecture (run uname -m on Linux/Mac OS or wmic os get OSArchitecture on Windows)
• compiler (run gcc --version or clang --version)

CentOS Linux 7 x86_64 with gcc 4.8.5

Please specify the steps taken to generate the issue, the command you are running and the relevant output.

I have encountered an issue with samtools markdup running past 8 days without actually completing on a few BAMs. I don’t get any relevant output since it just doesn’t finish. Digging deeper, I found out that a ~400 bp region in chromosome 2, with more than 8 million reads, is causing this issue. It looks like markdup just isn't optimized to deal with abnormally high depth regions, unless, I missed some parameter that would help. I have created micro BAMs of that region (with an additional 500bp on both ends) and tried running markdup on them but I still get the same results. For both types of BAMs, I used the command (BAM names were replaced with "micro"):

samtools markdup \
    -d “2500” \
    -S \
    -f “micro.samtools.markdup.txt” \
    --threads 4 \
    --write-index \
    -T “micro” \
    “micro.bam” \
    “micro.md.bam”

Also, I ran GATK MarkDuplicates (v4.1.8.0) on these micro BAMs and they finished under 35 minutes. The GATK command I used was the following:

gatk MarkDuplicates \
    --java-options “-Xmx28G” \
    --TMP_DIR “temp” \
    --ASSUME_SORT_ORDER coordinate \
    --CLEAR_DT false \
    --ADD_PG_TAG_TO_READS false \
    --OPTICAL_DUPLICATE_PIXEL_DISTANCE “2500” \
    --INPUT "micro.bam" \
    --METRICS_FILE “micro.gatk.mdmetrics.txt” \
    --OUTPUT “micro.md.bam”

If needed, I could provide a micro BAM that is causing this issue. Thank you.