Could not load dynamic library

[Arkadiy-Garber]

Getting some errors, likely not caused by the program but by my system, so jsut wondering if you have a solution:

~/bin/DeepMP$ DeepMP combine-extraction -fr docs/reads/untreated/ -re docs/output_example/error_features/untreated/tmp/ -rp docs/ref/Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.dna.toplevel.fa -ml 1 -cpu 24 -m CG -dn docs/output_example/error_features/untreated/dict_reads.pkl -o docs/output_example/untreated_features.tsv

2023-02-24 10:59:55.378422: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F AVX512_VNNI FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2023-02-24 10:59:55.536443: I tensorflow/core/util/port.cc:104] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable TF_ENABLE_ONEDNN_OPTS=0. 2023-02-24 10:59:56.391902: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: :/data/MAB/miniconda3/envs/deepmp_2021/lib/ 2023-02-24 10:59:56.392003: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: :/data/MAB/miniconda3/envs/deepmp_2021/lib/ 2023-02-24 10:59:56.392012: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly. INFO:root:Reading fast5 folder... 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 55676.60it/s] 3 fast5 files in total Parsing motifs string... Reading genome reference file... Getting features from nanopore reads... Writing features to file... finishing the writing process.. 3 of 3 fast5 files failed.. extract_features costs 0.2 seconds..

[Arkadiy-Garber]

So I got around the initial error by the following fix: https://stackoverflow.com/questions/74956134/could-not-load-dynamic-library-libnvinfer-so-7

but still "3 of r fast5 files failed.."

~/bin/DeepMP$ DeepMP combine-extraction -fr docs/reads/untreated/ -re docs/output_example/error_features/untreated/tmp/ -rp docs/ref/Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.dna.toplevel.fa -ml 1 -cpu 24 -m CG -dn docs/output_example/error_features/untreated/dict_reads.pkl -o docs/output_example/untreated_features.tsv

2023-02-24 12:42:09.243442: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F AVX512_VNNI FMA

To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.

2023-02-24 12:42:09.398899: I tensorflow/core/util/port.cc:104] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable TF_ENABLE_ONEDNN_OPTS=0. INFO:root:Reading fast5 folder... 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 56425.61it/s] 3 fast5 files in total Parsing motifs string... Reading genome reference file... Getting features from nanopore reads... Writing features to file... finishing the writing process.. 3 of 3 fast5 files failed.. extract_features costs 5.2 seconds..

[mandichen]

Hi Arkadiy, This issue is not caused by TensorFlow. It seems like the files are not parsed properly, could be the formatting. @pepebonet would you have a look at this?

[pepebonet]

Hi Arkadiy,

As Mandi that looks like some information that tensorflow is giving but there is no information about an actual error. Could you provide me with the setup of your environment by doing, for instance:

pip freeze

So that I can try to check whether I can reproduce the fact that reads are not being parsed. Thank you in advance.

Pepe