/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_011623_699_2033 + echo pp20240117_011623_699_2033 ++ id -u ++ id -g + docker run --name pp20240117_011623_699_2033 -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 16:16:28.392455: 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 16:16:28.988075: 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 . . . 2024-01-16 16:16:37.392644: I tensorflow/stream_executor/cuda/cuda_dnn.cc:366] Loaded cuDNN version 8100 WARNING:tensorflow:5 out of the last 5 calls to .predict_function at 0x7fc784213d30> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has experimental_relax_shapes=True option that relaxes argument shapes that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for more details. WARNING:tensorflow:5 out of the last 5 calls to .predict_function at 0x7fc784213d30> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has experimental_relax_shapes=True option that relaxes argument shapes that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for more details. + post_processing + '[' 1 = 1 ']' + rm -f /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~SpliceAI/pp-singularity-flag + '[' '' = y ']' + echo 0 + exit