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PopicLab / cue

Deep learning framework for SV calling and genotyping
MIT License
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installation error #30

Open leon945945 opened 6 months ago

leon945945 commented 6 months ago

Hi, I followed the instruction to install cue, but pycocotools threw an error, please give me some suggestions about how to fix it, thanks.

Building wheels for collected packages: pycocotools Building wheel for pycocotools (PEP 517) ... error ERROR: Command errored out with exit status 1: command: /home/songlizhi/software/cue/env/bin/python3.7 /home/songlizhi/software/cue/env/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /tmp/tmp7jj20tsb cwd: /tmp/pip-install-dx7jbz7q/pycocotools Complete output (23 lines): running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-cpython-37 creating build/lib.linux-x86_64-cpython-37/pycocotools copying pycocotools/init.py -> build/lib.linux-x86_64-cpython-37/pycocotools copying pycocotools/coco.py -> build/lib.linux-x86_64-cpython-37/pycocotools copying pycocotools/cocoeval.py -> build/lib.linux-x86_64-cpython-37/pycocotools copying pycocotools/mask.py -> build/lib.linux-x86_64-cpython-37/pycocotools running build_ext Compiling pycocotools/_mask.pyx because it changed. [1/1] Cythonizing pycocotools/_mask.pyx building 'pycocotools._mask' extension creating build/common creating build/temp.linux-x86_64-cpython-37 creating build/temp.linux-x86_64-cpython-37/common creating build/temp.linux-x86_64-cpython-37/pycocotools gcc -pthread -B /home/songlizhi/software/miniforge-pypy3/envs/py37/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-stm9n5lm/overlay/lib/python3.7/site-packages/numpy/core/include -I./common -I/home/songlizhi/software/cue/env/include -I/home/songlizhi/software/miniforge-pypy3/envs/py37/include/python3.7m -c ../common/maskApi.c -o build/temp.linux-x86_64-cpython-37/../common/maskApi.o -Wno-cpp -Wno-unused-function -std=c99 gcc: error: ../common/maskApi.c: No such file or directory /tmp/pip-build-env-stm9n5lm/overlay/lib/python3.7/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-dx7jbz7q/pycocotools/pycocotools/_mask.pyx tree = Parsing.p_module(s, pxd, full_module_name) error: command '/usr/bin/gcc' failed with exit code 1

ERROR: Failed building wheel for pycocotools Failed to build pycocotools ERROR: Could not build wheels for pycocotools which use PEP 517 and cannot be installed directly

leon945945 commented 6 months ago

Hi, I successfully instal cue by change the pycocorools 2.0.4 to pycocotools 2.0.6, but no results were generated after job finished. This is the log file:

  • cue (v0.2.2): discovery mode *

    [INFO] ========== Model config ========== model_path: /home/songlizhi/software/cue-0.2.2/data/models/cue.v2.pt gpu_ids: [] n_jobs_per_gpu: 1 n_cpus: 8 report_interval: 100 batch_size: 16 logging_level: INFO signal_set: SV_SIGNAL_SET.SHORT class_set: SV_CLASS_SET.BASIC5ZYG num_keypoints: 1 model_architecture: HG image_dim: 256 sigma: 10 stride: 4 heatmap_peak_threshold: 0.4 pretrained_refinenn_path: None config_file: call_model.yaml experiment_dir: /home/songlizhi/software/cue-0.2.2 devices: [device(type='cpu'), device(type='cpu'), device(type='cpu'), device(type='cpu'), device(type='cpu'), device(type='cpu'), device(type='cpu'), device(type='cpu')] device: cpu log_dir: /home/songlizhi/software/cue-0.2.2/logs/ report_dir: /home/songlizhi/software/cue-0.2.2/reports/ log_file: /home/songlizhi/software/cue-0.2.2/logs/main.log classes: ['NEG', 'DEL-HOM', 'INV-HOM', 'DUP-HOM', 'DEL-HET', 'INV-HET', 'DUP-HET', 'IDUP-HOM', 'IDUP-HET'] num_classes: 9 n_signals: 6 [INFO] ========== Data config ========= bam: /home02/songlizhi/sports/hifi/gxmy/align/phase/RFGX.GXmerge.bam fai: /home02/songlizhi/sports/hifi/gxmy/assembly/HiC/3d-DNA/WFGX-merge/r0/review/WFGX-merge.chromosome.chrUn.fa.fai chr_names: None logging_level: INFO n_cpus: 1 min_refine_buffer: 2000 refine_buffer_frac_size: 5 refine_pair_dist_frac_size: 2 refine_bp_kernels: [0, 50, 500] refine_min_support: 2 refine_disable: False min_pair_support: 2 min_pair_distance: 4000 max_pair_distance: 1000000 scan_target_intervals: True stream: True view_mode: False store_img: False empty_annotation: False bins_per_block: 8000 min_sv_len: 4000 min_qual_score: 50 bam_type: BAM_TYPE.SHORT signal_set: SV_SIGNAL_SET.SHORT signal_set_origin: SHORT bed: None blacklist_bed: None signal_vmax: {'RD': 600, 'RD_LOW': 800, 'RD_CLIPPED': 600, 'SM': 200, 'SR_RP': 600, 'LR': 600, 'LLRR': 100, 'RL': 100, 'LLRR_VS_LR': 1} signal_mapq: {'RD': 20, 'RD_LOW': 0, 'RD_CLIPPED': 20, 'SM': 20, 'SR_RP': 0, 'LR': 0, 'LLRR': 1, 'RL': 1, 'LLRR_VS_LR': 1} bin_size: 750 interval_size: 150000 step_size: 50000 shift_size: None heatmap_dim: 1000 image_dim: 256 class_set: SV_CLASS_SET.BASIC5ZYG num_keypoints: 1 bbox_padding: 0 config_file: call_data.yaml dataset_dir: /home/songlizhi/software/cue-0.2.2 info_dir: /home/songlizhi/software/cue-0.2.2/info/ image_dir: /home/songlizhi/software/cue-0.2.2/images/ annotation_dir: /home/songlizhi/software/cue-0.2.2/annotations/ annotated_images_dir: /home/songlizhi/software/cue-0.2.2/annotated_images/ classes: ['NEG', 'DEL-HOM', 'INV-HOM', 'DUP-HOM', 'DEL-HET', 'INV-HET', 'DUP-HET', 'IDUP-HOM', 'IDUP-HET'] num_classes: 9 num_signals: 6 uid: 0000000000 log_file: /home/songlizhi/software/cue-0.2.2/info/main.log [INFO] Running on 8 CPUs/GPUs [INFO] Chromosome lists processed by each process: [array(['chrUn', 'chr7'], dtype='<U5'), array(['chr9', 'chr1'], dtype='<U5'), array(['chr3'], dtype='<U5'), array(['chr4'], dtype='<U5'), array(['chr5'], dtype='<U5'), array(['chr6'], dtype='<U5'), array(['chr8'], dtype='<U5'), array(['chr2'], dtype='<U5')] INFO:root:Loaded model: /home/songlizhi/software/cue-0.2.2/data/models/cue.v2.pt on cpu INFO:root:Generating AUX index: /home02/songlizhi/sports/hifi/gxmy/align/phase/RFGX.GXmerge.bam.chr8.750.SHORT.auxindex INFO:root:Loaded model: /home/songlizhi/software/cue-0.2.2/data/models/cue.v2.pt on cpu INFO:root:Generating AUX index: /home02/songlizhi/sports/hifi/gxmy/align/phase/RFGX.GXmerge.bam.chr6.750.SHORT.auxindex INFO:root:Loaded model: /home/songlizhi/software/cue-0.2.2/data/models/cue.v2.pt on cpu INFO:root:Generating AUX index: /home02/songlizhi/sports/hifi/gxmy/align/phase/RFGX.GXmerge.bam.chrUn.750.SHORT.auxindex INFO:root:Loaded model: /home/songlizhi/software/cue-0.2.2/data/models/cue.v2.pt on cpu INFO:root:Generating AUX index: /home02/songlizhi/sports/hifi/gxmy/align/phase/RFGX.GXmerge.bam.chr3.750.SHORT.auxindex INFO:root:Loaded model: /home/songlizhi/software/cue-0.2.2/data/models/cue.v2.pt on cpu INFO:root:Generating AUX index: /home02/songlizhi/sports/hifi/gxmy/align/phase/RFGX.GXmerge.bam.chr4.750.SHORT.auxindex INFO:root:Loaded model: /home/songlizhi/software/cue-0.2.2/data/models/cue.v2.pt on cpu INFO:root:Generating AUX index: /home02/songlizhi/sports/hifi/gxmy/align/phase/RFGX.GXmerge.bam.chr2.750.SHORT.auxindex INFO:root:Loaded model: /home/songlizhi/software/cue-0.2.2/data/models/cue.v2.pt on cpu INFO:root:Generating AUX index: /home02/songlizhi/sports/hifi/gxmy/align/phase/RFGX.GXmerge.bam.chr5.750.SHORT.auxindex INFO:root:Loaded model: /home/songlizhi/software/cue-0.2.2/data/models/cue.v2.pt on cpu INFO:root:Generating AUX index: /home02/songlizhi/sports/hifi/gxmy/align/phase/RFGX.GXmerge.bam.chr9.750.SHORT.auxindex INFO:root:Number of bins: 31716 INFO:root:Number of bins: 47752 INFO:root:Number of bins: 34717 INFO:root:Number of bins: 44288 INFO:root:Number of bins: 46505 INFO:root:Number of bins: 50107 INFO:root:Number of bins: 43361 INFO:root:Number of bins: 66125 INFO:root:Selected 0 intervals INFO:root:Selected 0 interval pairs out of 0 pairs INFO:root:Selected 0 intervals INFO:root:Selected 0 interval pairs out of 0 pairs INFO:root:Processed 31299 reads INFO:root:Generating SV predictions for chr6 INFO:root:Number of target interval pairs: 0 INFO:root:Selected 0 intervals INFO:root:Selected 0 interval pairs out of 0 pairs INFO:root:Selected 0 intervals INFO:root:Selected 0 interval pairs out of 0 pairs INFO:root:Selected 0 intervals INFO:root:Selected 0 interval pairs out of 0 pairs INFO:root:Processed 39280 reads INFO:root:Generating SV predictions for chr2 INFO:root:Number of target interval pairs: 0 INFO:root:Selected 0 intervals INFO:root:Selected 0 interval pairs out of 0 pairs INFO:root:Processed 43079 reads INFO:root:Generating SV predictions for chr4 INFO:root:Number of target interval pairs: 0 INFO:root:Processed 52655 reads INFO:root:Generating SV predictions for chr8 INFO:root:Number of target interval pairs: 0 INFO:root:Selected 0 intervals INFO:root:Selected 0 interval pairs out of 0 pairs INFO:root:Processed 44961 reads INFO:root:Generating SV predictions for chr9 INFO:root:Number of target interval pairs: 0 INFO:root:Generating AUX index: /home02/songlizhi/sports/hifi/gxmy/align/phase/RFGX.GXmerge.bam.chr1.750.SHORT.auxindex INFO:root:Processed 52109 reads INFO:root:Generating SV predictions for chr3 INFO:root:Number of target interval pairs: 0 INFO:root:Processed 60624 reads INFO:root:Generating SV predictions for chr5 INFO:root:Number of target interval pairs: 0 INFO:root:Number of bins: 43552 INFO:root:Selected 0 intervals INFO:root:Selected 0 interval pairs out of 0 pairs INFO:root:Processed 41898 reads INFO:root:Generating SV predictions for chr1 INFO:root:Number of target interval pairs: 0 INFO:root:Selected 0 intervals INFO:root:Selected 0 interval pairs out of 0 pairs INFO:root:Processed 156506 reads INFO:root:Generating SV predictions for chrUn INFO:root:Number of target interval pairs: 0 INFO:root:Generating AUX index: /home02/songlizhi/sports/hifi/gxmy/align/phase/RFGX.GXmerge.bam.chr7.750.SHORT.auxindex INFO:root:Number of bins: 38920 INFO:root:Selected 0 intervals INFO:root:Selected 0 interval pairs out of 0 pairs INFO:root:Processed 39791 reads INFO:root:Generating SV predictions for chr7 INFO:root:Number of target interval pairs: 0 Processed 0 reads Read: 31299 reads Filtered: 0 reads Processed 0 reads Read: 43079 reads Filtered: 0 reads Processed 0 reads Read: 39280 reads Filtered: 0 reads Processed 0 reads Read: 52655 reads Filtered: 0 reads Processed 0 reads Read: 52109 reads Filtered: 0 reads Processed 0 reads Read: 60624 reads Filtered: 0 reads Processed 0 reads Read: 44961 reads Filtered: 0 reads Processed 0 reads Read: 41898 reads Filtered: 0 reads Processed 0 reads Read: 156506 reads Filtered: 0 reads Processed 0 reads Read: 39791 reads Filtered: 0 reads