Error in training a consensus network

[ziels]

I am trying to conduct the Walkthrough on my machine to train a consensus network using the example data and commands given here: https://nanoporetech.github.io/medaka/

I am encountering the following error when I try to run 'hp_compress':
$ hp_compress features ${CALLS2DRAFT}.bam ${TRAINFEATURES} -T ${TRUTH2DRAFT}.bam -t ${NUM_THREADS} -r ${REFNAME}:-${TRAINEND} --batch_size ${BATCHSIZE} --read_fraction ${FRACTION} --chunk_len 1000 --chunk_ovlp 0 -m ${MODEL_FEAT_OPT} --max_label_len 1

Using TensorFlow backend.
{'consensus_as_ref': False, 'is_compressed': False, 'log_min': None, 'max_hp_len': 1, 'normalise': 'total', 'ref_mode': None, 'with_depth': False}
[17:00:31 - root] FeatureEncoder options:
consensus_as_ref: False
is_compressed: False
log_min: None
max_hp_len: 1
normalise: total
ref_mode: None
with_depth: False
[17:00:31 - root] Got regions:
utg000001c:0-3762624
[17:00:32 - root] Processed utg000001c:3620001.0-3630000.0 (median depth 13.0)
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:476: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:481: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
[17:00:33 - root] Processed utg000001c:40001.0-50000.0 (median depth 15.0)
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:476: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:481: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
[17:00:33 - root] Processed utg000001c:3160001.0-3170000.0 (median depth 18.0)
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:476: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:481: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
[17:00:34 - root] Processed utg000001c:2110001.0-2120000.0 (median depth 32.0)
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:476: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:481: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
[17:00:34 - root] Processed utg000001c:1150001.0-1160000.0 (median depth 40.0)
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:476: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:481: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
[17:00:34 - root] Processed utg000001c:3660001.0-3670000.1 (median depth 19.0)
[17:00:35 - root] Processed utg000001c:3730001.0-3740000.1 (median depth 45.0)
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:476: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:481: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
[17:00:35 - root] Processed utg000001c:380001.0-390000.0 (median depth 12.0)
[17:00:36 - root] Processed utg000001c:2440001.0-2450000.1 (median depth 43.0)
[17:00:36 - root] Processed utg000001c:220001.0-230000.1 (median depth 26.0)
[17:00:36 - root] Processed utg000001c:2230001.0-2240000.1 (median depth 73.0)
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:476: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:481: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
[17:00:37 - root] Processed utg000001c:320001.0-330000.0 (median depth 57.0)
[17:00:37 - root] Processed utg000001c:36198.0-40000.1 (median depth 47.0)
[17:00:38 - root] Processed utg000001c:1220001.0-1230000.0 (median depth 9.0)
[17:00:38 - root] Processed utg000001c:620001.0-630000.1 (median depth 48.0)
[17:00:38 - root] Processed utg000001c:2660001.0-2670000.1 (median depth 100.0)
[17:00:38 - root] Processed utg000001c:2420001.0-2428111.0 (median depth 28.0)
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:476: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py:481: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
yield a[slicee]
[17:00:38 - root] Processed utg000001c:2428112.0-2430000.0 (median depth 8.0)
[17:00:39 - root] Processed utg000001c:1460001.0-1470000.1 (median depth 58.0)
[17:00:40 - root] Processed utg000001c:1600001.0-1610000.0 (median depth 28.0)
[17:00:41 - root] Processed utg000001c:3050001.0-3060000.2 (median depth 92.0)
[17:00:41 - root] Processed utg000001c:1800001.0-1810000.0 (median depth 18.0)
[17:00:42 - root] Processed utg000001c:3450001.0-3460000.1 (median depth 44.0)
[17:00:42 - root] Processed utg000001c:2980001.0-2990000.0 (median depth 55.0)
[17:00:42 - root] Processed utg000001c:3000001.0-3010000.0 (median depth 76.0)
[17:00:43 - root] Processed utg000001c:3330001.0-3340000.1 (median depth 80.0)
[17:00:43 - root] Processed utg000001c:1550001.0-1560000.0 (median depth 23.0)
[17:00:44 - root] Processed utg000001c:3520001.0-3530000.1 (median depth 82.0)
[17:00:44 - root] Processed utg000001c:3750001.0-3760000.0 (median depth 63.0)
[17:00:44 - root] Processed utg000001c:1610001.0-1620000.2 (median depth 32.0)
[17:00:45 - root] Processed utg000001c:3190001.0-3200000.0 (median depth 36.0)
[17:00:46 - root] Processed utg000001c:2450001.0-2460000.0 (median depth 42.0)
[17:00:46 - root] Processed utg000001c:480001.0-490000.1 (median depth 71.0)
[17:00:46 - root] Processed utg000001c:660001.0-670000.3 (median depth 58.0)
[17:00:47 - root] Processed utg000001c:1990001.0-2000000.0 (median depth 40.0)
[17:00:47 - root] Processed utg000001c:2460001.0-2470000.1 (median depth 38.0)
[17:00:48 - root] Processed utg000001c:3130001.0-3140000.1 (median depth 69.0)
[17:00:48 - root] Processed utg000001c:1330001.0-1331747.1 (median depth 78.0)
[17:00:48 - root] Processed utg000001c:300001.0-310000.0 (median depth 46.0)
[17:00:49 - root] Processed utg000001c:2280001.0-2290000.0 (median depth 29.0)
[17:00:49 - root] Processed utg000001c:1670001.0-1680000.0 (median depth 74.0)
[17:00:49 - root] Filtering removed all alignments of truth to ref from Region(ref_name='utg000001c', start=20000, end=30000).
[17:00:49 - root] Processed utg000001c:890001.0-900000.0 (median depth 25.0)
[17:00:51 - root] Processed utg000001c:60001.0-70000.0 (median depth 22.0)
[17:00:51 - root] Processed utg000001c:350001.0-360000.0 (median depth 35.0)
[17:00:51 - root] Processed utg000001c:3170001.0-3180000.1 (median depth 72.0)
[17:00:52 - root] Processed utg000001c:1331748.0-1340000.0 (median depth 75.0)
[17:00:52 - root] Processed utg000001c:3340001.0-3344122.2 (median depth 47.0)
[17:00:53 - root] Processed utg000001c:2590001.0-2600000.1 (median depth 93.0)
[17:00:53 - root] Processed utg000001c:1570001.0-1580000.1 (median depth 16.0)
[17:00:54 - root] Processed utg000001c:1940001.0-1950000.0 (median depth 88.0)
[17:00:54 - root] Processed utg000001c:1830035.0-1840000.0 (median depth 67.0)
[17:00:54 - root] Processed utg000001c:3460001.0-3470000.0 (median depth 41.0)
[17:00:55 - root] Processed utg000001c:610001.0-620000.0 (median depth 20.0)
[17:00:55 - root] Processed utg000001c:3344123.0-3350000.0 (median depth 47.0)
[17:00:55 - root] Processed utg000001c:1050001.0-1060000.2 (median depth 51.0)
[17:00:55 - root] Processed utg000001c:2970001.0-2980000.0 (median depth 85.0)
[17:00:56 - root] Processed utg000001c:3040001.0-3045139.0 (median depth 39.0)
[17:00:56 - root] Processed utg000001c:970001.0-980000.0 (median depth 6.0)
[17:00:57 - root] Processed utg000001c:2010001.0-2020000.1 (median depth 26.0)
[17:00:57 - root] Processed utg000001c:2840001.0-2845841.0 (median depth 45.0)
[17:00:57 - root] Processed utg000001c:720001.0-730000.1 (median depth 38.0)
[17:00:57 - root] Processed utg000001c:1680001.0-1690000.0 (median depth 45.0)
[17:00:58 - root] Processed utg000001c:2640001.0-2646413.0 (median depth 35.0)
[17:00:58 - root] Processed utg000001c:3045140.0-3050000.1 (median depth 54.0)
[17:00:58 - root] Processed utg000001c:2646414.0-2650000.0 (median depth 22.0)
[17:00:59 - root] Processed utg000001c:2845842.0-2850000.1 (median depth 60.0)
[17:00:59 - root] Processed utg000001c:1390001.0-1400000.0 (median depth 81.0)
[17:01:00 - root] Processed utg000001c:3010001.0-3020000.0 (median depth 67.0)
[17:01:00 - root] Processed utg000001c:450001.0-460000.0 (median depth 31.0)
[17:01:00 - root] Processed utg000001c:1560001.0-1570000.2 (median depth 51.0)
[17:01:01 - root] Processed utg000001c:3260001.0-3270000.0 (median depth 51.0)
[17:01:01 - root] Processed utg000001c:1030001.0-1032827.0 (median depth 14.0)
[17:01:01 - root] Processed utg000001c:2610001.0-2620000.0 (median depth 37.0)
[17:01:01 - root] Processed utg000001c:570001.0-580000.0 (median depth 68.0)
[17:01:01 - root] Processed utg000001c:1580001.0-1590000.4 (median depth 17.0)
[17:01:02 - root] Processed utg000001c:2700001.0-2710000.1 (median depth 45.0)
[17:01:03 - root] Processed utg000001c:1032828.0-1040000.4 (median depth 34.0)
[17:01:03 - root] Processed utg000001c:1540001.0-1550000.0 (median depth 18.0)
[17:01:03 - root] Processed utg000001c:290001.0-300000.0 (median depth 23.0)
[17:01:03 - root] Processed utg000001c:2690001.0-2700000.1 (median depth 76.0)
[17:01:05 - root] Processed utg000001c:3640001.0-3643166.0 (median depth 39.0)
[17:01:05 - root] Processed utg000001c:1280001.0-1290000.2 (median depth 58.0)
[17:01:05 - root] Processed utg000001c:1110001.0-1120000.0 (median depth 15.0)
[17:01:05 - root] Processed utg000001c:3110001.0-3120000.1 (median depth 43.0)
[17:01:05 - root] Processed utg000001c:990001.0-1000000.1 (median depth 68.0)
[17:01:05 - root] Processed utg000001c:3530001.0-3540000.0 (median depth 24.0)
[17:01:06 - root] Processed utg000001c:2000001.0-2010000.0 (median depth 45.0)
[17:01:06 - root] Processed utg000001c:460001.0-470000.0 (median depth 17.0)
[17:01:06 - root] Processed utg000001c:1650001.0-1660000.1 (median depth 14.0)
[17:01:06 - root] Processed utg000001c:2730001.0-2740000.0 (median depth 43.0)
[17:01:07 - root] Processed utg000001c:70001.0-80000.2 (median depth 14.0)
[17:01:07 - root] Processed utg000001c:3643167.0-3650000.1 (median depth 50.0)
[17:01:07 - root] Processed utg000001c:110001.0-120000.0 (median depth 33.0)
[17:01:08 - root] Processed utg000001c:2360001.0-2370000.0 (median depth 28.0)
[17:01:09 - root] Processed utg000001c:2120001.0-2129059.0 (median depth 43.0)
[17:01:10 - root] Processed utg000001c:180001.0-190000.1 (median depth 57.0)
[17:01:10 - root] Processed utg000001c:2370001.0-2380000.1 (median depth 73.0)
[17:01:10 - root] Processed utg000001c:2190001.0-2200000.0 (median depth 22.0)
[17:01:11 - root] Processed utg000001c:590001.0-600000.1 (median depth 14.0)
[17:01:11 - root] Processed utg000001c:560001.0-570000.2 (median depth 63.0)
[17:01:11 - root] Filtering removed all alignments of truth to ref from Region(ref_name='utg000001c', start=0, end=10000).
[17:01:11 - root] Processed utg000001c:1250001.0-1260000.0 (median depth 61.0)
[17:01:11 - root] Processed utg000001c:2040001.0-2050000.1 (median depth 18.0)
[17:01:12 - root] Processed utg000001c:2670001.0-2680000.0 (median depth 65.0)
[17:01:12 - root] Processed utg000001c:1200001.0-1210000.0 (median depth 11.0)
[17:01:12 - root] Processed utg000001c:2070001.0-2080000.0 (median depth 29.0)
[17:01:13 - root] Processed utg000001c:3410001.0-3420000.2 (median depth 82.0)
[17:01:13 - root] Filtering removed all alignments of truth to ref from Region(ref_name='utg000001c', start=2560000, end=2570000).
[17:01:14 - root] Processed utg000001c:50001.0-60000.1 (median depth 43.0)
[17:01:14 - root] Processed utg000001c:1410001.0-1420000.0 (median depth 27.0)
[17:01:14 - root] Filtering removed all alignments of truth to ref from Region(ref_name='utg000001c', start=10000, end=20000).
[17:01:15 - root] Processed utg000001c:260001.0-270000.2 (median depth 9.0)
[17:01:15 - root] Processed utg000001c:780001.0-790000.2 (median depth 53.0)
[17:01:16 - root] Processed utg000001c:740001.0-750000.3 (median depth 58.0)
[17:01:16 - root] Processed utg000001c:2860001.0-2870000.1 (median depth 82.0)
[17:01:16 - root] Processed utg000001c:2300001.0-2310000.0 (median depth 26.0)
[17:01:16 - root] Processed utg000001c:3140001.0-3144796.2 (median depth 83.0)
[17:01:17 - root] Processed utg000001c:1230001.0-1232100.1 (median depth 54.0)
[17:01:17 - root] Processed utg000001c:3490001.0-3500000.1 (median depth 77.0)
[17:01:17 - root] Processed utg000001c:540001.0-550000.0 (median depth 8.0)
[17:01:17 - root] Processed utg000001c:90001.0-100000.2 (median depth 77.0)
[17:01:18 - root] Processed utg000001c:3144797.0-3150000.1 (median depth 47.0)
[17:01:19 - root] Processed utg000001c:2490001.0-2500000.0 (median depth 33.0)
[17:01:19 - root] Processed utg000001c:3740001.0-3742853.1 (median depth 74.0)
[17:01:20 - root] Processed utg000001c:1730367.0-1740000.3 (median depth 67.0)
[17:01:20 - root] Processed utg000001c:1232101.0-1240000.0 (median depth 55.0)
[17:01:20 - root] Processed utg000001c:1340001.0-1350000.5 (median depth 58.0)
[17:01:20 - root] Processed utg000001c:680001.0-690000.1 (median depth 45.0)
[17:01:21 - root] Processed utg000001c:2630001.0-2640000.3 (median depth 54.0)
[17:01:21 - root] Processed utg000001c:1530001.0-1531081.2 (median depth 66.0)
[17:01:21 - root] Processed utg000001c:130001.0-135808.0 (median depth 72.0)
[17:01:22 - root] Processed utg000001c:270001.0-280000.2 (median depth 15.0)
[17:01:22 - root] Processed utg000001c:1531082.0-1540000.0 (median depth 11.0)
[17:01:22 - root] Processed utg000001c:520001.0-530000.0 (median depth 37.0)
[17:01:23 - root] Processed utg000001c:135809.0-140000.3 (median depth 37.0)
[17:01:23 - root] Processed utg000001c:3742855.0-3750000.2 (median depth 77.0)
[17:01:23 - root] Processed utg000001c:3550001.0-3560000.1 (median depth 15.0)
[17:01:24 - root] Processed utg000001c:3710001.0-3720000.3 (median depth 76.0)
[17:01:24 - root] Processed utg000001c:360001.0-370000.1 (median depth 68.0)
[17:01:25 - root] Processed utg000001c:950001.0-960000.0 (median depth 25.0)
[17:01:25 - root] Processed utg000001c:1500001.0-1510000.0 (median depth 19.0)
[17:01:25 - root] Processed utg000001c:1100001.0-1110000.0 (median depth 26.0)
[17:01:26 - root] Processed utg000001c:2790001.0-2800000.0 (median depth 54.0)
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[17:01:27 - root] Processed utg000001c:1130001.0-1132473.1 (median depth 70.0)
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[17:01:27 - root] Processed utg000001c:3630001.0-3640000.2 (median depth 99.0)
[17:01:28 - root] Processed utg000001c:3380001.0-3390000.0 (median depth 25.0)
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[17:01:30 - root] Processed utg000001c:1132474.0-1140000.1 (median depth 57.0)
[17:01:30 - root] Processed utg000001c:3480001.0-3490000.2 (median depth 71.0)
[17:01:30 - root] Processed utg000001c:420001.0-430000.0 (median depth 31.0)
[17:01:30 - root] Processed utg000001c:940001.0-950000.1 (median depth 38.0)
[17:01:30 - root] Processed utg000001c:3430001.0-3440000.1 (median depth 71.0)
[17:01:31 - root] Processed utg000001c:1970001.0-1980000.0 (median depth 28.0)
[17:01:31 - root] Processed utg000001c:3650001.0-3660000.0 (median depth 10.0)
[17:01:32 - root] Processed utg000001c:1190001.0-1200000.1 (median depth 16.0)
[17:01:32 - root] Processed utg000001c:550001.0-560000.0 (median depth 23.0)
[17:01:32 - root] Processed utg000001c:1070001.0-1080000.1 (median depth 35.0)
[17:01:33 - root] Processed utg000001c:2500001.0-2510000.1 (median depth 18.0)
[17:01:33 - root] Processed utg000001c:2400001.0-2410000.0 (median depth 70.0)
[17:01:34 - root] Processed utg000001c:1910001.0-1920000.0 (median depth 64.0)
[17:01:35 - root] Processed utg000001c:3670001.0-3680000.5 (median depth 58.0)
[17:01:35 - root] Processed utg000001c:2600001.0-2610000.1 (median depth 36.0)
[17:01:35 - root] Processed utg000001c:1400001.0-1410000.3 (median depth 49.0)
[17:01:36 - root] Processed utg000001c:1180001.0-1190000.2 (median depth 68.0)
[17:01:36 - root] Processed utg000001c:3420001.0-3430000.0 (median depth 39.0)
[17:01:37 - root] Processed utg000001c:410001.0-420000.1 (median depth 26.0)
[17:01:38 - root] Processed utg000001c:3270001.0-3280000.0 (median depth 86.0)
[17:01:38 - root] Processed utg000001c:1820001.0-1830000.0 (median depth 74.0)
[17:01:38 - root] Processed utg000001c:830001.0-833529.0 (median depth 15.0)
[17:01:38 - root] Processed utg000001c:500001.0-510000.0 (median depth 44.0)
[17:01:39 - root] Processed utg000001c:2960001.0-2970000.2 (median depth 71.0)
[17:01:39 - root] Processed utg000001c:710001.0-720000.0 (median depth 9.0)
[17:01:39 - root] Processed utg000001c:1090001.0-1100000.1 (median depth 61.0)
[17:01:39 - root] Processed utg000001c:2210001.0-2220000.0 (median depth 49.0)
[17:01:40 - root] Processed utg000001c:2520001.0-2527743.2 (median depth 65.0)
[17:01:40 - root] Processed utg000001c:790001.0-800000.0 (median depth 9.0)
[17:01:40 - root] Processed utg000001c:2510001.0-2520000.0 (median depth 18.0)
[17:01:40 - root] Processed utg000001c:1470001.0-1480000.0 (median depth 35.0)
[17:01:41 - root] Processed utg000001c:833530.0-840000.2 (median depth 70.0)
[17:01:43 - root] Processed utg000001c:2581818.0-2590000.0 (median depth 43.0)
[17:01:44 - root] Processed utg000001c:3070001.0-3080000.1 (median depth 67.0)
[17:01:44 - root] Processed utg000001c:1310001.0-1320000.0 (median depth 74.0)
[17:01:44 - root] Processed utg000001c:840001.0-850000.3 (median depth 58.0)
[17:01:45 - root] Processed utg000001c:1270001.0-1280000.1 (median depth 65.0)
[17:01:45 - root] Processed utg000001c:3080001.0-3090000.1 (median depth 89.0)
[17:01:45 - root] Processed utg000001c:1740001.0-1750000.4 (median depth 77.0)
[17:01:46 - root] Processed utg000001c:310001.0-320000.0 (median depth 41.0)
[17:01:46 - root] Processed utg000001c:1210001.0-1220000.0 (median depth 18.0)
[17:01:46 - root] Processed utg000001c:1000001.0-1010000.0 (median depth 19.0)
[17:01:47 - root] Processed utg000001c:170001.0-180000.0 (median depth 27.0)
[17:01:47 - root] Processed utg000001c:2200001.0-2210000.4 (median depth 82.0)
[17:01:48 - root] Processed utg000001c:2100001.0-2110000.1 (median depth 28.0)
[17:01:48 - root] Processed utg000001c:3700001.0-3710000.1 (median depth 33.0)
[17:01:49 - root] Processed utg000001c:2910001.0-2920000.0 (median depth 39.0)
[17:01:49 - root] Processed utg000001c:2920001.0-2930000.1 (median depth 58.0)
[17:01:49 - root] Processed utg000001c:3470001.0-3480000.2 (median depth 70.0)
[17:01:50 - root] Processed utg000001c:1490001.0-1500000.1 (median depth 11.0)
[17:01:50 - root] Processed utg000001c:3300001.0-3310000.1 (median depth 48.0)
[17:01:50 - root] Processed utg000001c:1770001.0-1780000.0 (median depth 11.0)
[17:01:51 - root] Processed utg000001c:750001.0-760000.0 (median depth 10.0)
[17:01:51 - root] Processed utg000001c:1790001.0-1800000.2 (median depth 62.0)
[17:01:52 - root] Processed utg000001c:860001.0-870000.1 (median depth 55.0)
[17:01:52 - root] Processed utg000001c:2890001.0-2900000.2 (median depth 84.0)
[17:01:52 - root] Processed utg000001c:1860001.0-1870000.1 (median depth 56.0)
[17:01:53 - root] Processed utg000001c:2930001.0-2940000.0 (median depth 28.0)
[17:01:53 - root] Processed utg000001c:2900001.0-2910000.0 (median depth 56.0)
[17:01:55 - root] Processed utg000001c:1850001.0-1860000.1 (median depth 20.0)
[17:01:55 - root] Processed utg000001c:2180001.0-2190000.2 (median depth 52.0)
[17:01:55 - root] Processed utg000001c:2770001.0-2780000.0 (median depth 45.0)
[17:01:55 - root] Processed utg000001c:2150001.0-2160000.0 (median depth 62.0)
[17:01:55 - root] Filtering removed all alignments of truth to ref from Region(ref_name='utg000001c', start=2550000, end=2560000).
[17:01:55 - root] Processed utg000001c:2780001.0-2790000.1 (median depth 46.0)
[17:01:56 - root] Processed utg000001c:1320001.0-1330000.0 (median depth 39.0)
[17:01:56 - root] Processed utg000001c:1920001.0-1929745.0 (median depth 56.0)
[17:01:56 - root] Processed utg000001c:1170001.0-1180000.0 (median depth 57.0)
[17:01:56 - root] Processed utg000001c:3200001.0-3210000.0 (median depth 16.0)
[17:01:56 - root] Processed utg000001c:240001.0-250000.0 (median depth 21.0)
[17:01:57 - root] Processed utg000001c:2060001.0-2070000.2 (median depth 15.0)
[17:01:57 - root] Processed utg000001c:3390001.0-3400000.0 (median depth 13.0)
[17:01:58 - root] Processed utg000001c:630001.0-634255.1 (median depth 53.0)
[17:01:58 - root] Processed utg000001c:800001.0-810000.0 (median depth 53.0)
[17:01:59 - root] Processed utg000001c:3560001.0-3570000.0 (median depth 37.0)
[17:02:00 - root] Processed utg000001c:1840001.0-1850000.2 (median depth 61.0)
[17:02:00 - root] Processed utg000001c:3060001.0-3070000.0 (median depth 72.0)
[17:02:00 - root] Processed utg000001c:1380001.0-1390000.0 (median depth 17.0)
[17:02:00 - root] Processed utg000001c:2620001.0-2630000.4 (median depth 48.0)
[17:02:00 - root] Processed utg000001c:3570001.0-3580000.0 (median depth 43.0)
[17:02:00 - root] Filtering removed all alignments of truth to ref from Region(ref_name='utg000001c', start=2540000, end=2550000).
[17:02:01 - root] Processed utg000001c:1780001.0-1790000.0 (median depth 21.0)
[17:02:01 - root] Processed utg000001c:634256.0-640000.1 (median depth 69.0)
[17:02:01 - root] Processed utg000001c:510001.0-520000.0 (median depth 11.0)
[17:02:02 - root] Processed utg000001c:1660001.0-1670000.1 (median depth 62.0)
[17:02:02 - root] Processed utg000001c:3240001.0-3244456.2 (median depth 63.0)
[17:02:03 - root] Processed utg000001c:2320001.0-2328420.0 (median depth 59.0)
[17:02:03 - root] Processed utg000001c:3680001.0-3690000.0 (median depth 34.0)
[17:02:04 - root] Processed utg000001c:3244457.0-3250000.0 (median depth 29.0)
[17:02:04 - root] Processed utg000001c:2328421.0-2330000.2 (median depth 56.0)
[17:02:05 - root] Processed utg000001c:900001.0-910000.1 (median depth 54.0)
[17:02:05 - root] Processed utg000001c:650001.0-660000.1 (median depth 43.0)
[17:02:05 - root] Processed utg000001c:1710001.0-1720000.2 (median depth 67.0)
[17:02:05 - root] Processed utg000001c:3370001.0-3380000.2 (median depth 55.0)
[17:02:06 - root] Processed utg000001c:1960001.0-1970000.1 (median depth 88.0)
[17:02:07 - root] Processed utg000001c:3250001.0-3260000.0 (median depth 25.0)
[17:02:07 - root] Processed utg000001c:2470001.0-2480000.0 (median depth 11.0)
[17:02:07 - root] Processed utg000001c:160001.0-170000.0 (median depth 29.0)
[17:02:07 - root] Processed utg000001c:2850001.0-2860000.0 (median depth 49.0)
[17:02:08 - root] Processed utg000001c:3610001.0-3620000.0 (median depth 59.0)
[17:02:08 - root] Processed utg000001c:3580001.0-3590000.1 (median depth 15.0)
[17:02:09 - root] Processed utg000001c:820001.0-830000.0 (median depth 62.0)
[17:02:09 - root] Processed utg000001c:3280001.0-3290000.2 (median depth 65.0)
[17:02:10 - root] Processed utg000001c:1950001.0-1960000.0 (median depth 30.0)
[17:02:10 - root] Processed utg000001c:1510001.0-1520000.0 (median depth 18.0)
[17:02:10 - root] Processed utg000001c:3020001.0-3030000.0 (median depth 76.0)
[17:02:10 - root] Processed utg000001c:190001.0-200000.3 (median depth 47.0)
[17:02:10 - root] Processed utg000001c:980001.0-990000.1 (median depth 23.0)
[17:02:11 - root] Processed utg000001c:2350001.0-2360000.0 (median depth 18.0)
[17:02:11 - root] Processed utg000001c:1450001.0-1460000.0 (median depth 66.0)
[17:02:12 - root] Processed utg000001c:2260001.0-2270000.0 (median depth 26.0)
[17:02:12 - root] Processed utg000001c:2710001.0-2720000.0 (median depth 64.0)
[17:02:12 - root] Processed utg000001c:530001.0-534557.0 (median depth 57.0)
[17:02:12 - root] Processed utg000001c:3030001.0-3040000.0 (median depth 45.0)
[17:02:13 - root] Processed utg000001c:534558.0-540000.0 (median depth 10.0)
[17:02:13 - root] Processed utg000001c:2820001.0-2830000.1 (median depth 40.0)
[17:02:14 - root] Processed utg000001c:1360001.0-1370000.0 (median depth 24.0)
[17:02:14 - root] Processed utg000001c:80001.0-90000.0 (median depth 39.0)
[17:02:15 - root] Processed utg000001c:1140001.0-1150000.1 (median depth 52.0)
[17:02:16 - root] Processed utg000001c:1480001.0-1490000.1 (median depth 75.0)
[17:02:16 - root] Processed utg000001c:1370001.0-1380000.2 (median depth 45.0)
[17:02:16 - root] Processed utg000001c:2680001.0-2690000.1 (median depth 57.0)
[17:02:16 - root] Processed utg000001c:580001.0-590000.0 (median depth 31.0)
[17:02:16 - root] Processed utg000001c:2390001.0-2400000.1 (median depth 41.0)
[17:02:17 - root] Processed utg000001c:1870001.0-1880000.0 (median depth 32.0)
[17:02:17 - root] Processed utg000001c:440001.0-450000.0 (median depth 20.0)
[17:02:17 - root] Processed utg000001c:2330001.0-2340000.0 (median depth 68.0)
[17:02:18 - root] Processed utg000001c:2760001.0-2770000.0 (median depth 10.0)
[17:02:18 - root] Processed utg000001c:2250001.0-2260000.0 (median depth 15.0)
[17:02:19 - root] Processed utg000001c:2140001.0-2150000.0 (median depth 12.0)
[17:02:19 - root] Processed utg000001c:470001.0-480000.0 (median depth 39.0)
[17:02:19 - root] Processed utg000001c:1880001.0-1890000.0 (median depth 35.0)
[17:02:20 - root] Processed utg000001c:880001.0-890000.0 (median depth 15.0)
[17:02:21 - root] Processed utg000001c:1690001.0-1700000.2 (median depth 21.0)
[17:02:21 - root] Processed utg000001c:3230001.0-3240000.0 (median depth 68.0)
[17:02:21 - root] Processed utg000001c:3540001.0-3543504.1 (median depth 36.0)
[17:02:22 - root] Processed utg000001c:1440001.0-1450000.2 (median depth 75.0)
[17:02:22 - root] Processed utg000001c:3760001.0-3762623.1 (median depth 20.0)
[17:02:22 - root] Processed utg000001c:1890001.0-1900000.2 (median depth 81.0)
[17:02:23 - root] Processed utg000001c:1620001.0-1630000.1 (median depth 53.0)
[17:02:23 - root] Processed utg000001c:3180001.0-3190000.1 (median depth 72.0)
[17:02:24 - root] Processed utg000001c:1420001.0-1430000.0 (median depth 92.0)
[17:02:24 - root] Processed utg000001c:2430001.0-2440000.0 (median depth 36.0)
[17:02:24 - root] Processed utg000001c:3543505.0-3550000.1 (median depth 69.0)
[17:02:25 - root] Processed utg000001c:2750001.0-2760000.4 (median depth 50.0)
[17:02:25 - root] Processed utg000001c:850001.0-860000.0 (median depth 69.0)
[17:02:25 - root] Processed utg000001c:910001.0-920000.0 (median depth 41.0)
[17:02:27 - root] Processed utg000001c:370001.0-380000.0 (median depth 13.0)
[17:02:27 - root] Processed utg000001c:1010001.0-1020000.0 (median depth 19.0)
[17:02:27 - root] Processed utg000001c:1930001.0-1940000.1 (median depth 61.0)
[17:02:27 - root] Processed utg000001c:2160001.0-2170000.0 (median depth 40.0)
[17:02:28 - root] Processed utg000001c:2080001.0-2090000.0 (median depth 55.0)
[17:02:29 - root] Processed utg000001c:920001.0-930000.0 (median depth 21.0)
[17:02:29 - root] Processed utg000001c:1630747.0-1640000.1 (median depth 64.0)
[17:02:29 - root] Processed utg000001c:330001.0-335222.0 (median depth 45.0)
[17:02:29 - root] Processed utg000001c:640001.0-650000.0 (median depth 28.0)
[17:02:29 - root] Processed utg000001c:335223.0-340000.0 (median depth 7.0)
[17:02:30 - root] Processed utg000001c:1300001.0-1310000.1 (median depth 102.0)
[17:02:30 - root] Processed utg000001c:150001.0-160000.0 (median depth 20.0)
[17:02:31 - root] Processed utg000001c:3320001.0-3330000.1 (median depth 79.0)
[17:02:31 - root] Processed utg000001c:3590001.0-3600000.0 (median depth 33.0)
[17:02:31 - root] Processed utg000001c:1020001.0-1030000.0 (median depth 21.0)
[17:02:31 - root] Processed utg000001c:2480001.0-2490000.1 (median depth 26.0)
[17:02:32 - root] Processed utg000001c:2340001.0-2350000.1 (median depth 75.0)
[17:02:33 - root] Processed utg000001c:140001.0-150000.0 (median depth 4.0)
[17:02:33 - root] Processed utg000001c:390001.0-400000.2 (median depth 43.0)
[17:02:34 - root] Processed utg000001c:1290001.0-1300000.1 (median depth 72.0)
[17:02:34 - root] Processed utg000001c:1040001.0-1050000.1 (median depth 33.0)
[17:02:35 - root] Processed utg000001c:2880001.0-2890000.1 (median depth 21.0)
[17:02:35 - root] Processed utg000001c:3210001.0-3220000.1 (median depth 60.0)
[17:02:35 - root] Processed utg000001c:2220001.0-2228768.0 (median depth 14.0)
[17:02:35 - root] Processed utg000001c:690001.0-700000.1 (median depth 59.0)
[17:02:35 - root] Processed utg000001c:2228769.0-2230000.1 (median depth 38.0)
[17:02:36 - root] Processed utg000001c:3360001.0-3370000.1 (median depth 76.0)
[17:02:37 - root] Processed utg000001c:960001.0-970000.1 (median depth 58.0)
[17:02:37 - root] Filtering removed all alignments of truth to ref from Region(ref_name='utg000001c', start=2530000, end=2540000).
[17:02:37 - root] Processed utg000001c:2130001.0-2140000.0 (median depth 94.0)
[17:02:38 - root] Processed utg000001c:870001.0-880000.2 (median depth 68.0)
[17:02:39 - root] Processed utg000001c:2950001.0-2960000.0 (median depth 45.0)
[17:02:39 - root] Processed utg000001c:1060001.0-1070000.0 (median depth 46.0)
[17:02:40 - root] Processed utg000001c:2940001.0-2945532.2 (median depth 78.0)
[17:02:40 - root] Processed utg000001c:670001.0-680000.0 (median depth 23.0)
[17:02:40 - root] Processed utg000001c:1520001.0-1530000.0 (median depth 21.0)
[17:02:41 - root] Filtering removed all alignments of truth to ref from Region(ref_name='utg000001c', start=2570000, end=2580000).
[17:02:41 - root] Processed utg000001c:1240001.0-1250000.1 (median depth 88.0)
[17:02:41 - root] Processed utg000001c:3500001.0-3510000.1 (median depth 97.0)
[17:02:41 - root] Processed utg000001c:1590001.0-1600000.2 (median depth 102.0)
[17:02:42 - root] Processed utg000001c:2945533.0-2950000.0 (median depth 44.0)
[17:02:42 - root] Processed utg000001c:1980001.0-1990000.2 (median depth 75.0)
[17:02:42 - root] Processed utg000001c:930001.0-933194.0 (median depth 17.0)
[17:02:43 - root] Processed utg000001c:3600001.0-3610000.0 (median depth 25.0)
[17:02:43 - root] Processed utg000001c:2800001.0-2810000.0 (median depth 5.0)
[17:02:43 - root] Processed utg000001c:2090001.0-2100000.0 (median depth 23.0)
[17:02:43 - root] Processed utg000001c:933195.0-940000.3 (median depth 25.0)
[17:02:44 - root] Processed utg000001c:430001.0-434861.0 (median depth 59.0)
[17:02:44 - root] Processed utg000001c:770001.0-780000.0 (median depth 64.0)
[17:02:44 - root] Processed utg000001c:434862.0-440000.0 (median depth 6.0)
[17:02:44 - root] Processed utg000001c:3150001.0-3160000.1 (median depth 54.0)
[17:02:45 - root] Processed utg000001c:3290001.0-3300000.2 (median depth 44.0)
[17:02:46 - root] Processed utg000001c:2870001.0-2880000.0 (median depth 26.0)
[17:02:46 - root] Processed utg000001c:2020001.0-2029389.0 (median depth 16.0)
[17:02:46 - root] Processed utg000001c:200001.0-210000.2 (median depth 35.0)
[17:02:46 - root] Processed utg000001c:3120001.0-3130000.0 (median depth 17.0)
[17:02:47 - root] Processed utg000001c:2270001.0-2280000.1 (median depth 9.0)
[17:02:47 - root] Processed utg000001c:1120001.0-1130000.0 (median depth 55.0)
[17:02:47 - root] Processed utg000001c:490001.0-500000.0 (median depth 21.0)
[17:02:48 - root] Processed utg000001c:3690001.0-3700000.0 (median depth 55.0)
[17:02:48 - root] Processed utg000001c:1700001.0-1710000.1 (median depth 84.0)
[17:02:48 - root] Processed utg000001c:3720001.0-3730000.0 (median depth 53.0)
[17:02:48 - root] Processed utg000001c:230001.0-235528.0 (median depth 50.0)
[17:02:50 - root] Processed utg000001c:235529.0-240000.0 (median depth 37.0)
[17:02:50 - root] Processed utg000001c:730001.0-733907.0 (median depth 55.0)
[17:02:50 - root] Processed utg000001c:733908.0-740000.0 (median depth 10.0)
[17:02:50 - root] Processed utg000001c:280001.0-290000.0 (median depth 27.0)
[17:02:50 - root] Processed utg000001c:1720001.0-1730000.0 (median depth 26.0)
[17:02:51 - root] Processed utg000001c:1080001.0-1090000.2 (median depth 20.0)
[17:02:52 - root] Processed utg000001c:2740001.0-2746118.0 (median depth 22.0)
[17:02:52 - root] Processed utg000001c:3400001.0-3410000.0 (median depth 70.0)
[17:02:52 - root] Processed utg000001c:2170001.0-2180000.0 (median depth 81.0)
[17:02:53 - root] Processed utg000001c:1350001.0-1360000.0 (median depth 100.0)
[17:02:53 - root] Processed utg000001c:3510001.0-3520000.0 (median depth 13.0)
[17:02:53 - root] Processed utg000001c:1430001.0-1431388.6 (median depth 20.0)
[17:02:53 - root] Processed utg000001c:2240001.0-2250000.1 (median depth 90.0)
[17:02:54 - root] Processed utg000001c:2746119.0-2750000.1 (median depth 64.0)
[17:02:54 - root] Processed utg000001c:760001.0-770000.0 (median depth 22.0)
[17:02:54 - root] Processed utg000001c:3310001.0-3320000.1 (median depth 51.0)
[17:02:54 - root] Processed utg000001c:1810001.0-1820000.0 (median depth 23.0)
[17:02:55 - root] Processed utg000001c:2290001.0-2300000.1 (median depth 22.0)
[17:02:55 - root] Processed utg000001c:1431389.0-1440000.3 (median depth 31.0)
[17:02:56 - root] Processed utg000001c:2380001.0-2390000.1 (median depth 14.0)
[17:02:56 - root] Processed utg000001c:1160001.0-1170000.0 (median depth 25.0)
[17:02:57 - root] Processed utg000001c:3440001.0-3443822.2 (median depth 62.0)
[17:02:57 - root] Processed utg000001c:3090001.0-3100000.0 (median depth 44.0)
[17:02:57 - root] Processed utg000001c:2650001.0-2660000.0 (median depth 109.0)
[17:02:58 - root] Processed utg000001c:3443823.0-3450000.0 (median depth 12.0)
[17:02:58 - root] Processed utg000001c:810001.0-820000.1 (median depth 36.0)
[17:02:59 - root] Processed utg000001c:2030001.0-2040000.0 (median depth 60.0)
[17:02:59 - root] Processed utg000001c:120001.0-130000.0 (median depth 15.0)
[17:02:59 - root] Processed utg000001c:2990001.0-3000000.1 (median depth 81.0)
[17:03:00 - root] Processed utg000001c:1900001.0-1910000.2 (median depth 74.0)
[17:03:00 - root] Processed utg000001c:100001.0-110000.0 (median depth 19.0)
[17:03:00 - root] Processed utg000001c:2410001.0-2420000.0 (median depth 58.0)
[17:03:00 - root] Processed utg000001c:1640001.0-1650000.0 (median depth 15.0)
[17:03:01 - root] Processed utg000001c:1760001.0-1770000.0 (median depth 38.0)
[17:03:02 - root] Processed utg000001c:2050001.0-2060000.0 (median depth 12.0)
[17:03:02 - root] Processed utg000001c:3100001.0-3110000.0 (median depth 44.0)
[17:03:03 - root] Processed utg000001c:210001.0-220000.4 (median depth 75.0)
[17:03:03 - root] Processed utg000001c:400001.0-410000.1 (median depth 80.0)
[17:03:04 - root] Processed utg000001c:250001.0-260000.0 (median depth 64.0)
[17:03:05 - root] Processed utg000001c:3350001.0-3360000.0 (median depth 18.0)
[17:03:06 - root] Processed utg000001c:1260001.0-1270000.0 (median depth 75.0)
[17:03:06 - root] Processed utg000001c:3220001.0-3230000.0 (median depth 82.0)
[17:03:06 - root] Processed utg000001c:2720001.0-2730000.0 (median depth 58.0)
[17:03:06 - root] Processed utg000001c:2830001.0-2840000.0 (median depth 64.0)
[17:03:07 - root] Processed utg000001c:1750001.0-1760000.1 (median depth 79.0)
[17:03:07 - root] Processed utg000001c:340001.0-350000.0 (median depth 68.0)
Traceback (most recent call last):
File "/home/ziels/virtual-envs/medaka/bin/hp_compress", line 11, in
sys.exit(main())
File "/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/compress.py", line 650, in main
args.func(args)
File "/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/compress.py", line 615, in choose_feature_func
training_batches(args)
File "/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/compress.py", line 514, in training_batches
write_yaml_data(fname, to_save)
File "/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/medaka/common.py", line 263, in write_yaml_data
hdf[group] = yaml.dump(d)
File "/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/yaml/init.py", line 217, in dump
return dump_all([data], stream, Dumper=Dumper, **kwds)
File "/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/yaml/init.py", line 196, in dump_all
dumper.represent(data)
File "/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/yaml/representer.py", line 26, in represent
node = self.represent_data(data)
File "/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/yaml/representer.py", line 57, in represent_data
node = self.yaml_representers[None](self, data)
File "/home/ziels/virtual-envs/medaka/lib/python3.6/site-packages/yaml/representer.py", line 229, in represent_undefined
raise RepresenterError("cannot represent an object", data)
yaml.representer.RepresenterError: ('cannot represent an object', Counter({4: 2748771, 1: 969842, 2: 954640, 0: 936965, 3: 933782}))

I am able to run medaka_consensus okay with the walkthrough dataset, and so I believe that medaka is installed okay. Do you have any ideas on what could be causing this yaml- associated error above?

Thanks!

[cjw85]

Hi @ziels,

We've not tested with Python 3.6, but I don't see that this should be an issue. Could you find the version of the yaml package that is installed, e.g.:

python -c "import yaml; print(yaml.__version__)"

[ziels]

Hi @cjw85, it looks like I have yaml version 4.1 installed:

$ python -c "import yaml; print(yaml.__version__)"

4.1

[cjw85]

It looks like there are issues with new versions of pyyaml, see here: yaml/pyyaml#193

I have 3.13 here, could you try installing that: pip install pyyaml==3.13

[ziels]

That seemed to do the trick, thanks!