Hello, I’m running minimap2 with hifi reads, but deepvariant is throwing errors downstream. I think the BAM file from minimap2 might be messed up.
nohup singularity exec --nv -B input:/input,output:/output/ \
/psd/container/singularity-3.8.6/clara-parabricks_v4.5.1-1.sif \
pbrun minimap2 --ref /input/ref.fna --in-fq /input/hifi.fq.gz --preset map-hifi \
--low-memory --num-threads 32 --read-group-sm beagle --read-group-id-prefix beagle \
--tmp-dir /output/pbruntmp --out-bam /output/beagles.bam --logfile /output/mm2.log
samtools quickcheck says it’s fine, but it fails when I try to build the index with samtools index.
# samtools quickcheck -vvv beagle.bam
verbosity set to 3
checking beagle.bam
opened beagle.bam
beagle.bam is sequence data
beagle.bam has 56 targets in header.
beagle.bam has good EOF block.
# samtools index beagle.bam
[E::bgzf_uncompress] Inflate operation failed: 1
[E::bgzf_read] Read block operation failed with error 1 after 13833 of 21913 bytes
samtools index: failed to create index for "beagle.bam"
Is there a way to solve it? Thank you
I used different hifi reads and the BAM file worked fine. Could it be that the fastq reads was too big and messed up the BAM format? The size of my fastq file (hifi.fq.gz) is 50G.
# nvidia-smi
Sun Sep 7 14:15:05 2025
+-----------------------------------------------------------------------------------------+
| NVIDIA-SMI 550.120 Driver Version: 550.120 CUDA Version: 12.4 |
|-----------------------------------------+------------------------+----------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+========================+======================|
| 0 NVIDIA RTX 4500 Ada Gene... Off | 00000000:2A:00.0 Off | Off |
| 30% 37C P8 9W / 210W | 10MiB / 24570MiB | 0% Default |
| | | N/A |
+-----------------------------------------+------------------------+----------------------+
+-----------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=========================================================================================|
| 0 N/A N/A 31804 G /usr/lib/xorg/Xorg 4MiB |
+-----------------------------------------------------------------------------------------+