TypeError: only integer tensors of a single element can be converted to an index
Opened this issue · 3 comments
shenweima commented
Traceback (most recent call last):
File "/share/home/yzbsl_masw/scripts/cue/engine/call.py", line 104, in <module>
_ = Parallel(n_jobs=n_procs)(
File "/share/home/yzbsl_masw/.conda/envs/cue/lib/python3.8/site-packages/joblib/parallel.py", line 1029, in __call__
if self.dispatch_one_batch(iterator):
File "/share/home/yzbsl_masw/.conda/envs/cue/lib/python3.8/site-packages/joblib/parallel.py", line 847, in dispatch_one_batch
self._dispatch(tasks)
File "/share/home/yzbsl_masw/.conda/envs/cue/lib/python3.8/site-packages/joblib/parallel.py", line 765, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File "/share/home/yzbsl_masw/.conda/envs/cue/lib/python3.8/site-packages/joblib/_parallel_backends.py", line 208, in apply_async
result = ImmediateResult(func)
File "/share/home/yzbsl_masw/.conda/envs/cue/lib/python3.8/site-packages/joblib/_parallel_backends.py", line 572, in __init__
self.results = batch()
File "/share/home/yzbsl_masw/.conda/envs/cue/lib/python3.8/site-packages/joblib/parallel.py", line 252, in __call__
return [func(*args, **kwargs)
File "/share/home/yzbsl_masw/.conda/envs/cue/lib/python3.8/site-packages/joblib/parallel.py", line 252, in <listcomp>
return [func(*args, **kwargs)
File "/share/home/yzbsl_masw/scripts/cue/engine/call.py", line 88, in call
predictions = core.evaluate(model, data_loader, config, device, output_dir=predictions_dir,
File "/share/home/yzbsl_masw/scripts/cue/engine/core.py", line 96, in evaluate
plotting.plot_images(images, predictions, range(len(images)), config.classes,
File "/share/home/yzbsl_masw/scripts/cue/img/plotting.py", line 202, in plot_images
image = annotate(image, targets[indices[i]], classes, display_boxes=True, color=(0, 76 / 255, 153 / 255))
File "/share/home/yzbsl_masw/scripts/cue/img/plotting.py", line 163, in annotate
cv2.circle(image, (p[0], p[1]), int(image_dim/100), color=(128/255, 128/255, 128/255),
TypeError: only integer tensors of a single element can be converted to an index
shenweima commented
this is config info
Job 5810276 has been submitted to the queue [cpu]. Command: /share/home/yzbsl_masw/scripts/cue.sh
Job 5810276 is waiting to be started...
Job 5810276 has started on host hw50.
*********************************
* cue (v0.2.2): discovery mode *
*********************************
[INFO] ========== Model config ==========
model_path: /share/home/yzbsl_masw/scripts/cue/data/models/cue.v2.pt
gpu_ids: []
n_jobs_per_gpu: 1
n_cpus: 1
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: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/SV_cue
devices: [device(type='cpu')]
device: cpu
log_dir: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/SV_cue/logs/
report_dir: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/SV_cue/reports/
log_file: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/SV_cue/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: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/1496A.mrkdup.sorted.cram
fai: /share/home/yzbsl_masw/data/genomes/ref/Chinese_spring2.1_KN9204_1RS.fasta.fai
chr_names: ['chr1A']
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: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/SV_cue
info_dir: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/SV_cue/info/
image_dir: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/SV_cue/images/
annotation_dir: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/SV_cue/annotations/
annotated_images_dir: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/SV_cue/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: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/SV_cue/info/main.log
[INFO] Running on 1 CPUs/GPUs
[INFO] Chromosome lists processed by each process: [array(['chr1A'], dtype='<U5')]
[INFO] Loaded model: /share/home/yzbsl_masw/scripts/cue/data/models/cue.v2.pt on cpu
[INFO] Loading AUX index: /share/home/yzbsl_masw/data/projects/results/CS2.1/AABBDD/1496A.mrkdup.sorted.cram.chr1A.750.SHORT.auxindex
[INFO] Generating SV predictions for chr1A
[INFO] Number of target interval pairs: 5776
[INFO] Interval pair: chr1A x=0 y=0
[INFO] Interval pair: chr1A x=0 y=50000
[INFO] Interval pair: chr1A x=0 y=100000
[INFO] Interval pair: chr1A x=0 y=150000
[INFO] Interval pair: chr1A x=0 y=200000
[INFO] Interval pair: chr1A x=0 y=250000
[INFO] Interval pair: chr1A x=0 y=300000
[INFO] Interval pair: chr1A x=0 y=350000
[INFO] Interval pair: chr1A x=0 y=400000
viq854 commented
Hi @shenweima,
I haven't encountered this issue before and need a bit more info to help debug this.
Everything seems good with the configs -- these are just default values with the custom cram and fasta index files, correct?
Could you also share the versions of the packages installed -- are you using the virtual environment install option or anything custom?
Thanks,
V
prmunn commented
Hi @viq854 and @shenweima - I got the same error and was able to work around it by casting p[0] and p[1] as integers on lines 161 and 163 of plotting.py
So, line 161 becomes:
cv2.circle(image, (int(p[0]), int(p[1])), int(image_dim/100), color=color, thickness=-thickness)
And line 163 becomes:
cv2.circle(image, (int(p[0]), int(p[1])), int(image_dim/100), color=(128/255, 128/255, 128/255), thickness=-thickness)
Hope this helps