Minimizer error related to vg giraffe

Healthcare & Life Sciences Parabricks
1

parabricks_giraffe_1875584.err.txt (68.7 KB)

Hi Developers,

I encountered an error while running parabricks giraffe in a singularity container (error log attached). I thought GPU memory was the issue so I tried adjusting by --memory-limit 20, yet the issue persisted.

A snippet of the error message: (full error message attached)

Read sequence: GCCACATTTTCTTTATCCAGTCTATCCAATCCCAATACTTTTGAGGCCAAGGCAAGAGGATTGCTTGAGCCCAGAAGTAGGAGACCAGCCTGGGCAACAGTGAGATTCTGTCTCTACAAAAATTTTTCAAAAATTAGCCAGTTATGGTGG
Read quality: FGFGGGGGGGFGGGGFFFFGGFFGGFFFGFFGGFGGGGGGGGG1GFGFFFFFFFFF@FFEFGGGGFG3FFGGHFFFFEFFFDGFEGFFGGGFFEEGGFGGFFEGBFGGGGGFGGGFFFGGGFFFFGGFHGGFFFGFGFHFGFGGFFEFFG
error[MinimizerMapper::faster_cap]: Minimizers seem impossible to disrupt in region 44 45 0 6
T0:     000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111
T0:     000000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444444
T0:     012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
T0:     AGAAAAGAAATATATAACCTTAAATTCACACATTGCAAAAGAAGAAACACCAAAGCCAGTAATCTAATATAAAGTTCCAGAAAAAGGGAATAAAACCCAATTCACTTTTGAAGCAGCATAACCTAGACAACAAAACTGGTTAAGAACATT
T0:     ----------TATATAACCTTAAATTCACACATTGCAAA---------- (#5, 1 hits)
T0:                ----------AAATTCACACATTGCAAAAGAAGAAACAC---------- (#0, 1 hits)
T0:                           ----------TACTGGCTTTGGTGTTTCTTCTTTTGCAA--------- (#4, 1 hits)
T0:                                     ----------TATATTAGATTACTGGCTTTGGTGTTTCT (#6, 1 hits)
T0:                                      ----------GAAACACCAAAGCCAGTAATCTAATATAA---------- (#3, 1 hits)
T0:                                                 ------TGGAACTTTATATTAGATTACTGGCTTTG---- (#8, 1 hits)
T0:                                                  ----------TTTTCTGGAACTTTATATTAGATTACTGG---------- (#10, 1 hits)
T0:                                                             ------ATTCCCTTTTTCTGGAACTTTATATTAGA---- (#1, 1 hits)
T0:                                                                                                ----------TTGTCTAGGTTATGCTGCTTCAAAAGTGA---------- (#9, 1 hits)
T0:                                                                                                           ------TGAAGCAGCATAACCTAGACAACAAAACT---- (#7, 1 hits)
T0:                                                                                                            ----------CAGCATAACCTAGACAACAAAACTGGTTA-------- (#2, 1 hits)
Mininizer 5 agg start 0 length 49 core start 10 length 29

The job was run on one L40S GPU:

+-----------------------------------------------------------------------------+
| NVIDIA-SMI 525.147.05   Driver Version: 525.147.05   CUDA Version: 12.0     |
|-------------------------------+----------------------+----------------------+
| 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 L40S         On   | 00000000:56:00.0 Off |                    0 |
| N/A   31C    P8    33W / 350W |      0MiB / 46068MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
|   1  NVIDIA L40S         On   | 00000000:57:00.0 Off |                    0 |
| N/A   33C    P8    32W / 350W |      0MiB / 46068MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
|   2  NVIDIA L40S         On   | 00000000:5B:00.0 Off |                    0 |
| N/A   32C    P8    32W / 350W |      0MiB / 46068MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
|   3  NVIDIA L40S         On   | 00000000:5C:00.0 Off |                    0 |
| N/A   34C    P8    35W / 350W |      0MiB / 46068MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+

The command executed is:

singularity run --nv \
     -B /group/paed_yangwl/hg38/pangenome/:/mnt/ref \
     -B "${DATA_DIR}":/mnt/data \
     -B "${OUTPUT}":/mnt/out \
     -B "${TEMP}":/tmp \
     --pwd /mnt/data \
     --cleanenv \
     /group/paed_yangwl/clara-parabricks_4.4.0-1.sif \
     pbrun giraffe \
     --read-group "${SAMPLE}"-RG1 \
     --sample "${SAMPLE}" \
     --read-group-library "${SAMPLE}"-L1 \
     --read-group-platform DNBSEQ \
     --read-group-pu pu \
     --dist-name /mnt/ref/hprc-v1.0-mc-grch38-minaf.0.1.dist \
     --minimizer-name /mnt/ref/hprc-v1.0-mc-grch38-minaf.0.1.min \
     --gbz-name /mnt/ref/hprc-v1.0-mc-grch38-minaf.0.1.gbz \
     --xg-name /mnt/ref/hprc-v1.0-mc-grch38-minaf.0.1.xg \
     --graph-name /mnt/ref/hprc-v1.0-mc-grch38-minaf.0.1.gg \
     --gbwt-name /mnt/ref/hprc-v1.0-mc-grch38-minaf.0.1.gbwt \
     --in-fq /mnt/data/$(basename "$FQ1") /mnt/data/$(basename "$FQ2") \
     --out-bam /mnt/out/"$SAMPLE".bqsr.bam \
     --memory-limit 20 \
     --low-memory \
     --gpuwrite \
     --tmp-dir /tmp

Any help will be greatly appreciated!