TypeError: only integer tensors of a single element can be converted to an index

[shenweima]

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]

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]

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]

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