Hi I am getting the following error with the latest GPU version of minimap2:
Run parameters:
docker run \
-v "$(dirname $(realpath {input.fq}))":"/mnt/input_fq" \
-v "$(dirname $(realpath {input.ref}))":"/mnt/input_ref" \
-v "$(dirname $(realpath {output.bam}))":"/mnt/output" \
--workdir /tmp \
--env TCMALLOC_MAX_TOTAL_THREAD_CACHE_BYTES=268435456 \
--user $(id -u):$(id -g) \
--rm \
--gpus {params.gpu} \
{params.container} \
pbrun minimap2 \
--ref "/mnt/input_ref/$(basename {input.ref})" \
--in-fq "/mnt/input_fq/$(basename {input.fq})" \
--out-bam "/mnt/output/$(basename {output.bam})" \
--num-chaining-threads 3 \
--preset map-ont \
--eqx \
--num-threads {threads} \
--alignment-large-pair-size 5000 \
--process-large-alignments-on-cpu \
--num-alignment-threads-per-gpu 8 \
--num-alignment-device-mem-buffers 8 \
--gpusort \
--num-gpus {resources.gpu} \
--gpuwrite
Logfile with Error message:
[PB Info 2024-Jun-05 15:30:46] 11.1 700000
[PB Info 2024-Jun-05 15:30:52] 11.2 700000
[PB Info 2024-Jun-05 15:30:58] 11.3 710000
[PB Info 2024-Jun-05 15:31:04] 11.4 720000
[PB Info 2024-Jun-05 15:31:10] 11.5 740000
[PB Info 2024-Jun-05 15:31:16] 11.6 750000
terminate called after throwing an instance of 'thrust::system::detail::bad_alloc'
what(): std::bad_alloc: cudaErrorInvalidValue: invalid argument
[PB e[31mErrore[0m 2024-Jun-05 15:31:21][-unknown-:0] Received signal: 6
For technical support visit https://docs.nvidia.com/clara/index.html#parabricks, exiting.
For technical support visit https://docs.nvidia.com/clara/index.html#parabricks
Exiting...
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation
Our server has two H100 GPUs
Hello Caspar, during which stage did you see this error? For example is it under the heading where a box is printed saying “Parabricks accelerated Genomics Pipeline Version 4.3.1-1 minimap2”?
Hi,
its in the first stage: Reading reference file
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /mnt/input_fq/TEST_TUE_01.SUP.fastq.gz
[Parabricks Options Mesg]:
@RG\tID:17b03957-a602-44a4-b3af-526a3b\tLB:lib1\tPL:bar\tSM:sample\tPU:17b03957-a602-44a4-b3af-526a3b
[PB Info 2024-Jun-05 15:17:59] ------------------------------------------------------------------------------
[PB Info 2024-Jun-05 15:17:59] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Jun-05 15:17:59] || Version 4.3.1-1 ||
[PB Info 2024-Jun-05 15:17:59] || minimap2 ||
[PB Info 2024-Jun-05 15:17:59] ------------------------------------------------------------------------------
[PB Info 2024-Jun-05 15:17:59] Reading reference file.
[PB Info 2024-Jun-05 15:19:40] -------------------------------------
[PB Info 2024-Jun-05 15:19:40] Elapsed-Minutes Processed-Reads
[PB Info 2024-Jun-05 15:19:40] -------------------------------------
[PB Info 2024-Jun-05 15:19:40] 0.0 0
[PB Info 2024-Jun-05 15:19:46] 0.1 0
[PB Info 2024-Jun-05 15:19:52] 0.2 0
[PB Info 2024-Jun-05 15:19:58] 0.3 0
[PB Info 2024-Jun-05 15:20:04] 0.4 0
[PB Info 2024-Jun-05 15:20:10] 0.5 0
[PB Info 2024-Jun-05 15:20:16] 0.6 0
[PB Info 2024-Jun-05 15:20:22] 0.7 0
[PB Info 2024-Jun-05 15:20:28] 0.8 0
[PB Info 2024-Jun-05 15:20:34] 0.9 0
[PB Info 2024-Jun-05 15:20:40] 1.0 0
[PB Info 2024-Jun-05 15:20:46] 1.1 0
[PB Info 2024-Jun-05 15:20:52] 1.2 0
[PB Info 2024-Jun-05 15:20:58] 1.3 0
[PB Info 2024-Jun-05 15:21:04] 1.4 0
[PB Info 2024-Jun-05 15:21:10] 1.5 0
[PB Info 2024-Jun-05 15:21:16] 1.6 0
[PB Info 2024-Jun-05 15:21:22] 1.7 0
[PB Info 2024-Jun-05 15:21:28] 1.8 0
[PB Info 2024-Jun-05 15:21:34] 1.9 10000
[PB Info 2024-Jun-05 15:21:40] 2.0 20000
[PB Info 2024-Jun-05 15:21:46] 2.1 20000
[PB Info 2024-Jun-05 15:21:52] 2.2 40000
[PB Info 2024-Jun-05 15:21:58] 2.3 40000
[PB Info 2024-Jun-05 15:22:04] 2.4 40000
[PB Info 2024-Jun-05 15:22:10] 2.5 50000
[PB Info 2024-Jun-05 15:22:16] 2.6 50000
[PB Info 2024-Jun-05 15:22:22] 2.7 60000
[PB Info 2024-Jun-05 15:22:28] 2.8 80000
[PB Info 2024-Jun-05 15:22:34] 2.9 80000
[PB Info 2024-Jun-05 15:22:40] 3.0 80000
[PB Info 2024-Jun-05 15:22:46] 3.1 90000
[PB Info 2024-Jun-05 15:22:52] 3.2 100000
[PB Info 2024-Jun-05 15:22:58] 3.3 110000
[PB Info 2024-Jun-05 15:23:04] 3.4 120000
[PB Info 2024-Jun-05 15:23:10] 3.5 120000
[PB Info 2024-Jun-05 15:23:16] 3.6 120000
[PB Info 2024-Jun-05 15:23:22] 3.7 130000
[PB Info 2024-Jun-05 15:23:28] 3.8 140000
[PB Info 2024-Jun-05 15:23:34] 3.9 150000
[PB Info 2024-Jun-05 15:23:40] 4.0 160000
[PB Info 2024-Jun-05 15:23:46] 4.1 160000
[PB Info 2024-Jun-05 15:23:52] 4.2 170000
[PB Info 2024-Jun-05 15:23:58] 4.3 180000
[PB Info 2024-Jun-05 15:24:04] 4.4 180000
[PB Info 2024-Jun-05 15:24:10] 4.5 180000
[PB Info 2024-Jun-05 15:24:16] 4.6 200000
[PB Info 2024-Jun-05 15:24:22] 4.7 200000
[PB Info 2024-Jun-05 15:24:28] 4.8 210000
[PB Info 2024-Jun-05 15:24:34] 4.9 210000
[PB Info 2024-Jun-05 15:24:40] 5.0 220000
[PB Info 2024-Jun-05 15:24:46] 5.1 220000
[PB Info 2024-Jun-05 15:24:52] 5.2 230000
[PB Info 2024-Jun-05 15:24:58] 5.3 240000
[PB Info 2024-Jun-05 15:25:04] 5.4 260000
[PB Info 2024-Jun-05 15:25:10] 5.5 260000
[PB Info 2024-Jun-05 15:25:16] 5.6 260000
[PB Info 2024-Jun-05 15:25:22] 5.7 270000
[PB Info 2024-Jun-05 15:25:28] 5.8 280000
[PB Info 2024-Jun-05 15:25:34] 5.9 300000
[PB Info 2024-Jun-05 15:25:40] 6.0 300000
[PB Info 2024-Jun-05 15:25:46] 6.1 300000
[PB Info 2024-Jun-05 15:25:52] 6.2 310000
[PB Info 2024-Jun-05 15:25:58] 6.3 320000
[PB Info 2024-Jun-05 15:26:04] 6.4 320000
[PB Info 2024-Jun-05 15:26:10] 6.5 330000
[PB Info 2024-Jun-05 15:26:16] 6.6 340000
[PB Info 2024-Jun-05 15:26:22] 6.7 360000
[PB Info 2024-Jun-05 15:26:28] 6.8 360000
[PB Info 2024-Jun-05 15:26:34] 6.9 360000
[PB Info 2024-Jun-05 15:26:40] 7.0 370000
[PB Info 2024-Jun-05 15:26:46] 7.1 370000
[PB Info 2024-Jun-05 15:26:52] 7.2 380000
[PB Info 2024-Jun-05 15:26:58] 7.3 380000
[PB Info 2024-Jun-05 15:27:04] 7.4 380000
[PB Info 2024-Jun-05 15:27:10] 7.5 380000
[PB Info 2024-Jun-05 15:27:16] 7.6 380000
[PB Info 2024-Jun-05 15:27:22] 7.7 380000
[PB Info 2024-Jun-05 15:27:28] 7.8 380000
[PB Info 2024-Jun-05 15:27:34] 7.9 380000
[PB Info 2024-Jun-05 15:27:40] 8.0 430000
[PB Info 2024-Jun-05 15:27:46] 8.1 450000
[PB Info 2024-Jun-05 15:27:52] 8.2 450000
[PB Info 2024-Jun-05 15:27:58] 8.3 470000
[PB Info 2024-Jun-05 15:28:04] 8.4 490000
[PB Info 2024-Jun-05 15:28:10] 8.5 490000
[PB Info 2024-Jun-05 15:28:16] 8.6 510000
[PB Info 2024-Jun-05 15:28:22] 8.7 510000
[PB Info 2024-Jun-05 15:28:28] 8.8 520000
[PB Info 2024-Jun-05 15:28:34] 8.9 530000
[PB Info 2024-Jun-05 15:28:40] 9.0 530000
[PB Info 2024-Jun-05 15:28:46] 9.1 540000
[PB Info 2024-Jun-05 15:28:52] 9.2 550000
[PB Info 2024-Jun-05 15:28:58] 9.3 560000
[PB Info 2024-Jun-05 15:29:04] 9.4 570000
[PB Info 2024-Jun-05 15:29:10] 9.5 570000
[PB Info 2024-Jun-05 15:29:16] 9.6 580000
[PB Info 2024-Jun-05 15:29:22] 9.7 580000
[PB Info 2024-Jun-05 15:29:28] 9.8 590000
[PB Info 2024-Jun-05 15:29:34] 9.9 600000
[PB Info 2024-Jun-05 15:29:40] 10.0 610000
[PB Info 2024-Jun-05 15:29:46] 10.1 630000
[PB Info 2024-Jun-05 15:29:52] 10.2 630000
[PB Info 2024-Jun-05 15:29:58] 10.3 630000
[PB Info 2024-Jun-05 15:30:04] 10.4 650000
[PB Info 2024-Jun-05 15:30:10] 10.5 650000
[PB Info 2024-Jun-05 15:30:16] 10.6 660000
[PB Info 2024-Jun-05 15:30:22] 10.7 670000
[PB Info 2024-Jun-05 15:30:28] 10.8 670000
[PB Info 2024-Jun-05 15:30:34] 10.9 690000
[PB Info 2024-Jun-05 15:30:40] 11.0 700000
[PB Info 2024-Jun-05 15:30:46] 11.1 700000
[PB Info 2024-Jun-05 15:30:52] 11.2 700000
[PB Info 2024-Jun-05 15:30:58] 11.3 710000
[PB Info 2024-Jun-05 15:31:04] 11.4 720000
[PB Info 2024-Jun-05 15:31:10] 11.5 740000
[PB Info 2024-Jun-05 15:31:16] 11.6 750000
terminate called after throwing an instance of 'thrust::system::detail::bad_alloc'
what(): std::bad_alloc: cudaErrorInvalidValue: invalid argument
[PB e[31mErrore[0m 2024-Jun-05 15:31:21][-unknown-:0] Received signal: 6
For technical support visit https://docs.nvidia.com/clara/index.html#parabricks, exiting.
For technical support visit https://docs.nvidia.com/clara/index.html#parabricks
Exiting...
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation
Could not run minimap2
Exiting pbrun ...
Thanks, Caspar
I can confirm that this issue has been resolved by now. I reran the whole basecalling pipeline for this dataset, so my current assumption is that the original FASTQ input was likely corrupted.
Thanks for your help, hope our inquiry did not spark too much investigations.
1 Like
system
August 6, 2024, 9:54am
5
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