A deep learning-based tool to identify splice variants. This tool needs NVIDIA GPU.
##fileformat=VCFv4.2
##fileDate=20191004
##reference=GRCh37/hg19
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
annotation~SpliceAI -c 8 -m 32 input_1/input.vcf
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20191004
##reference=GRCh37/hg19
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
pp annotation~SpliceAI -c 8 -m 32 input_1/input.vcf
PID: 252754
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'annotation~SpliceAI' -c 8 -m 32 input_1/input.vcf
Checking the realpath of input files.
0 input_1/input.vcf
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI
c2997108/tensorflow:2.7.1-gpu-spliceai_2 centos:centos6
using docker
+ set -o pipefail
++ echo input_1/input.vcf
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ cat SPLICEAI
++ basename SPLICEAI .vcf
cat: SPLICEAI: そのようなファイルやディレクトリはありません
+ FUNC_RUN_DOCKER_GPU c2997108/tensorflow:2.7.1-gpu-spliceai_2 spliceai -O SPLICEAI.spliceai.vcf -R /usr/local/db/hg38/hg38.fa -A grch38
+ PP_RUN_IMAGE=c2997108/tensorflow:2.7.1-gpu-spliceai_2
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20240117_010227_340_29281
+ echo pp20240117_010227_340_29281
++ id -u
++ id -g
+ docker run --name pp20240117_010227_340_29281 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI -u 2007:600 -i --rm --gpus all c2997108/tensorflow:2.7.1-gpu-spliceai_2 spliceai -O SPLICEAI.spliceai.vcf -R /usr/local/db/hg38/hg38.fa -A grch38
ERROR:root:invalid file `<_io.TextIOWrapper name='' mode='r' encoding='utf-8'>` (mode=`b'r'`) - is it VCF/BCF format?
++ onerror 27
++ status=1
++ script=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/annotation~SpliceAI
++ line=27
++ shift
++ set +x
------------------------------------------------------------
Error occured on /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/annotation~SpliceAI [Line 27]: Status 1
PID: 252756
User: yoshitake.kazutoshi
Current directory: /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI
Command line: /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/annotation~SpliceAI
------------------------------------------------------------
PID: 256033
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'annotation~SpliceAI' -c 8 -m 32 input_1/input.vcf
Checking the realpath of input files.
0 input_1/input.vcf
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI
c2997108/tensorflow:2.7.1-gpu-spliceai_2 centos:centos6
using docker
+ set -o pipefail
+ i=input_1/input.vcf
++ echo input_1/input.vcf
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ cat input_1/input.vcf
++ basename input_1/input.vcf .vcf
+ FUNC_RUN_DOCKER_GPU c2997108/tensorflow:2.7.1-gpu-spliceai_2 spliceai -O input.spliceai.vcf -R /usr/local/db/hg38/hg38.fa -A grch38
+ PP_RUN_IMAGE=c2997108/tensorflow:2.7.1-gpu-spliceai_2
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20240117_010524_804_6354
+ echo pp20240117_010524_804_6354
++ id -u
++ id -g
+ docker run --name pp20240117_010524_804_6354 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI -u 2007:600 -i --rm --gpus all c2997108/tensorflow:2.7.1-gpu-spliceai_2 spliceai -O input.spliceai.vcf -R /usr/local/db/hg38/hg38.fa -A grch38
2024-01-16 16:05:29.574623: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-01-16 16:05:30.197626: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1525] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 8094 MB memory: -> device: 0, name: NVIDIA GeForce RTX 3080, pci bus id: 0000:b3:00.0, compute capability: 8.6
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
WARNING:root:Skipping record (ref issue): 2 152389953 . T A,C,G . . .
WARNING:root:Skipping record (ref issue): 2 179446218 . ATACT A . . .
WARNING:root:Skipping record (ref issue): 2 179446218 . ATACT AT,ATA . . .
WARNING:root:Skipping record (ref issue): 2 179642185 . G A . . .
WARNING:root:Skipping record (ref issue): 19 38958362 . C T . . .
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit