installation error

[leon945945]

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]

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