2021-06-10 04:02:59 [INFO] Starting.
2021-06-10 04:02:59 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/
2021-06-10 04:02:59 [INFO] Creating new aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/aggregate.hdf5
2021-06-10 04:02:59 [INFO] Using chromosome sizes at /grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes
2021-06-10 04:02:59 [INFO] Using only main chromosomes: chr1, chr2, chr3, chr4, chr5, chr6, chr7, chrX, chr8, chr9, chr11, chr10, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr20, chr19, chrY, chr22, chr21, chrM
2021-06-10 04:03:00 [INFO] Building aggregate.
2021-06-10 04:03:00 [INFO] Writing every 10 Runs.
2021-06-10 04:03:00 [INFO] Processing SRX3031098. (1/5)
2021-06-10 04:03:00 [INFO] Processing SRX3031098-SRR5862508. (1/5)
2021-06-10 04:03:05 [INFO] Processing SRX3031096. (2/5)
2021-06-10 04:03:05 [INFO] Processing SRX3031096-SRR5862506. (2/5)
2021-06-10 04:03:10 [INFO] Processing SRX3031099. (3/5)
2021-06-10 04:03:10 [INFO] Processing SRX3031099-SRR5862509. (3/5)
2021-06-10 04:03:34 [INFO] Processing SRX3031097. (4/5)
2021-06-10 04:03:34 [INFO] Processing SRX3031097-SRR5862507. (4/5)
2021-06-10 04:03:42 [INFO] Processing SRX3031100. (5/5)
2021-06-10 04:03:42 [INFO] Processing SRX3031100-SRR5862510. (5/5)
2021-06-10 04:03:50 [INFO] Writing to disk...
2021-06-10 04:03:53 [INFO] Finished.
2021-08-02 17:08:55 [INFO] Starting.
2021-08-02 17:08:55 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/
2021-08-02 17:08:55 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/aggregate.hdf5
2021-08-02 17:08:55 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-02 17:08:56 [INFO] Building aggregate for 1bp_raw network.
2021-08-02 17:08:56 [INFO] Writing every 10 Runs.
2021-08-02 17:08:56 [INFO] Processing SRX3031098. (1/5)
2021-08-02 17:08:56 [INFO] Processing SRX3031098-SRR5862508. (1/5)
2021-08-02 17:22:55 [INFO] Processing SRX3031096. (2/5)
2021-08-02 17:22:55 [INFO] Processing SRX3031096-SRR5862506. (2/5)
2021-08-02 17:23:15 [ERROR] Adding SRR5862506:chr2_vs_chr2 to in memory aggregate failed. Error message:
Traceback (most recent call last):
  File "/grid/gillis/data/nfox/hi_c_data_processing/software/aggregate.py", line 428, in add_dataset
    aggregate_data[c] = aggregate_data[c] + net
  File "/grid/gillis/home/nfox/software/miniconda3/lib/python3.8/site-packages/scipy/sparse/base.py", line 415, in __add__
    return self._add_sparse(other)
  File "/grid/gillis/home/nfox/software/miniconda3/lib/python3.8/site-packages/scipy/sparse/compressed.py", line 359, in _add_sparse
    return self._binopt(other, '_plus_')
  File "/grid/gillis/home/nfox/software/miniconda3/lib/python3.8/site-packages/scipy/sparse/compressed.py", line 1226, in _binopt
    indptr = np.empty(self.indptr.shape, dtype=idx_dtype)
MemoryError: Unable to allocate 924. MiB for an array with shape (242193530,) and data type int32

2021-08-04 22:07:01 [INFO] Starting.
2021-08-04 22:07:01 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/
2021-08-04 22:07:01 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/aggregate.hdf5
2021-08-04 22:07:01 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-04 22:07:01 [INFO] Building aggregate for 1bp_raw network.
2021-08-04 22:07:01 [INFO] Writing every 10 Runs.
2021-08-04 22:07:01 [INFO] Processing SRX3031098. (1/5)
2021-08-04 22:07:01 [INFO] Processing SRX3031098-SRR5862508. (1/5)
2021-08-04 22:10:29 [INFO] Processing SRX3031096. (2/5)
2021-08-04 22:10:29 [INFO] Processing SRX3031096-SRR5862506. (2/5)
2021-08-04 22:18:02 [INFO] Processing SRX3031099. (3/5)
2021-08-04 22:18:02 [INFO] Processing SRX3031099-SRR5862509. (3/5)
2021-08-04 22:25:24 [INFO] Processing SRX3031097. (4/5)
2021-08-04 22:25:24 [INFO] Processing SRX3031097-SRR5862507. (4/5)
2021-08-04 22:32:50 [INFO] Processing SRX3031100. (5/5)
2021-08-04 22:32:50 [INFO] Processing SRX3031100-SRR5862510. (5/5)
2021-08-04 22:40:36 [INFO] Writing to disk...
2021-08-04 22:41:35 [INFO] Finished.
2021-08-12 14:31:17 [INFO] Starting.
2021-08-12 14:31:17 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/
2021-08-12 14:31:17 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/aggregate.hdf5
2021-08-12 14:31:17 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-12 14:31:18 [INFO] Building aggregate for 40kbp_raw network.
2021-08-12 14:31:18 [INFO] Writing every 10 Runs.
2021-08-12 14:31:18 [INFO] Processing SRX3031098. (1/5)
2021-08-12 14:31:18 [INFO] Processing SRX3031098-SRR5862508. (1/5)
2021-08-12 14:31:28 [INFO] Processing SRX3031096. (2/5)
2021-08-12 14:31:28 [INFO] Processing SRX3031096-SRR5862506. (2/5)
2021-08-12 14:31:43 [INFO] Processing SRX3031099. (3/5)
2021-08-12 14:31:43 [INFO] Processing SRX3031099-SRR5862509. (3/5)
2021-08-12 14:31:54 [INFO] Processing SRX3031097. (4/5)
2021-08-12 14:31:54 [INFO] Processing SRX3031097-SRR5862507. (4/5)
2021-08-12 14:32:04 [INFO] Processing SRX3031100. (5/5)
2021-08-12 14:32:04 [INFO] Processing SRX3031100-SRR5862510. (5/5)
2021-08-12 14:32:14 [INFO] Writing to disk...
2021-08-12 14:32:18 [INFO] Finished.
2021-08-12 15:10:18 [INFO] Starting.
2021-08-12 15:10:18 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/
2021-08-12 15:10:18 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/aggregate.hdf5
2021-08-12 15:10:18 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-12 15:10:19 [INFO] Building aggregate for 25kbp_raw network.
2021-08-12 15:10:19 [INFO] Writing every 10 Runs.
2021-08-12 15:10:19 [INFO] Processing SRX3031098. (1/5)
2021-08-12 15:10:19 [INFO] Processing SRX3031098-SRR5862508. (1/5)
2021-08-12 15:10:27 [INFO] Processing SRX3031096. (2/5)
2021-08-12 15:10:27 [INFO] Processing SRX3031096-SRR5862506. (2/5)
2021-08-12 15:10:37 [INFO] Processing SRX3031099. (3/5)
2021-08-12 15:10:37 [INFO] Processing SRX3031099-SRR5862509. (3/5)
2021-08-12 15:10:45 [INFO] Processing SRX3031097. (4/5)
2021-08-12 15:10:45 [INFO] Processing SRX3031097-SRR5862507. (4/5)
2021-08-12 15:10:53 [INFO] Processing SRX3031100. (5/5)
2021-08-12 15:10:53 [INFO] Processing SRX3031100-SRR5862510. (5/5)
2021-08-12 15:11:01 [INFO] Writing to disk...
2021-08-12 15:11:03 [INFO] Finished.
2021-08-12 15:44:39 [INFO] Starting.
2021-08-12 15:44:39 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/
2021-08-12 15:44:39 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/aggregate.hdf5
2021-08-12 15:44:39 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-12 15:44:40 [INFO] Building aggregate for 5kbp_raw network.
2021-08-12 15:44:40 [INFO] Writing every 10 Runs.
2021-08-12 15:44:40 [INFO] Processing SRX3031098. (1/5)
2021-08-12 15:44:40 [INFO] Processing SRX3031098-SRR5862508. (1/5)
2021-08-12 15:44:49 [INFO] Processing SRX3031096. (2/5)
2021-08-12 15:44:49 [INFO] Processing SRX3031096-SRR5862506. (2/5)
2021-08-12 15:45:01 [INFO] Processing SRX3031099. (3/5)
2021-08-12 15:45:01 [INFO] Processing SRX3031099-SRR5862509. (3/5)
2021-08-12 15:45:10 [INFO] Processing SRX3031097. (4/5)
2021-08-12 15:45:10 [INFO] Processing SRX3031097-SRR5862507. (4/5)
2021-08-12 15:45:19 [INFO] Processing SRX3031100. (5/5)
2021-08-12 15:45:19 [INFO] Processing SRX3031100-SRR5862510. (5/5)
2021-08-12 15:45:27 [INFO] Writing to disk...
2021-08-12 15:45:30 [INFO] Finished.
2021-08-12 16:33:28 [INFO] Starting.
2021-08-12 16:33:28 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/
2021-08-12 16:33:28 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/aggregate.hdf5
2021-08-12 16:33:28 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-12 16:33:29 [INFO] Building aggregate for 1kbp_raw network.
2021-08-12 16:33:29 [INFO] Writing every 10 Runs.
2021-08-12 16:33:29 [INFO] Processing SRX3031098. (1/5)
2021-08-12 16:33:29 [INFO] Processing SRX3031098-SRR5862508. (1/5)
2021-08-12 16:33:38 [INFO] Processing SRX3031096. (2/5)
2021-08-12 16:33:38 [INFO] Processing SRX3031096-SRR5862506. (2/5)
2021-08-12 16:33:51 [INFO] Processing SRX3031099. (3/5)
2021-08-12 16:33:51 [INFO] Processing SRX3031099-SRR5862509. (3/5)
2021-08-12 16:34:02 [INFO] Processing SRX3031097. (4/5)
2021-08-12 16:34:02 [INFO] Processing SRX3031097-SRR5862507. (4/5)
2021-08-12 16:34:13 [INFO] Processing SRX3031100. (5/5)
2021-08-12 16:34:13 [INFO] Processing SRX3031100-SRR5862510. (5/5)
2021-08-12 16:34:23 [INFO] Writing to disk...
2021-08-12 16:34:27 [INFO] Finished.
2021-08-20 17:59:20 [INFO] Starting.
2021-08-20 17:59:20 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/
2021-08-20 17:59:20 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/aggregate.hdf5
2021-08-20 17:59:20 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-20 17:59:21 [INFO] Building aggregate for 100kbp_raw network.
2021-08-20 17:59:21 [INFO] Writing every 10 Runs.
2021-08-20 17:59:21 [INFO] Processing SRX3031098. (1/5)
2021-08-20 17:59:21 [INFO] Processing SRX3031098-SRR5862508. (1/5)
2021-08-20 17:59:29 [INFO] Processing SRX3031096. (2/5)
2021-08-20 17:59:29 [INFO] Processing SRX3031096-SRR5862506. (2/5)
2021-08-20 17:59:39 [INFO] Processing SRX3031099. (3/5)
2021-08-20 17:59:39 [INFO] Processing SRX3031099-SRR5862509. (3/5)
2021-08-20 17:59:46 [INFO] Processing SRX3031097. (4/5)
2021-08-20 17:59:46 [INFO] Processing SRX3031097-SRR5862507. (4/5)
2021-08-20 17:59:55 [INFO] Processing SRX3031100. (5/5)
2021-08-20 17:59:55 [INFO] Processing SRX3031100-SRR5862510. (5/5)
2021-08-20 18:00:13 [INFO] Writing to disk...
2021-08-20 18:00:19 [INFO] Finished.
2021-08-23 11:30:30 [INFO] Starting.
2021-08-23 11:30:30 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/
2021-08-23 11:30:30 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/aggregate.hdf5
2021-08-23 11:30:30 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-23 11:30:31 [INFO] Building aggregate for 250kbp_raw network.
2021-08-23 11:30:31 [INFO] Writing every 10 Runs.
2021-08-23 11:30:31 [INFO] Processing SRX3031098. (1/5)
2021-08-23 11:30:31 [INFO] Processing SRX3031098-SRR5862508. (1/5)
2021-08-23 11:30:35 [INFO] Processing SRX3031096. (2/5)
2021-08-23 11:30:35 [INFO] Processing SRX3031096-SRR5862506. (2/5)
2021-08-23 11:30:43 [INFO] Processing SRX3031099. (3/5)
2021-08-23 11:30:43 [INFO] Processing SRX3031099-SRR5862509. (3/5)
2021-08-23 11:30:50 [INFO] Processing SRX3031097. (4/5)
2021-08-23 11:30:50 [INFO] Processing SRX3031097-SRR5862507. (4/5)
2021-08-23 11:30:56 [INFO] Processing SRX3031100. (5/5)
2021-08-23 11:30:56 [INFO] Processing SRX3031100-SRR5862510. (5/5)
2021-08-23 11:31:03 [INFO] Writing to disk...
2021-08-23 11:31:04 [INFO] Finished.
2021-08-23 13:16:52 [INFO] Starting.
2021-08-23 13:16:52 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/
2021-08-23 13:16:52 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP113478/aggregate.hdf5
2021-08-23 13:16:52 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-23 13:16:53 [INFO] Building aggregate for 500kbp_raw network.
2021-08-23 13:16:53 [INFO] Writing every 10 Runs.
2021-08-23 13:16:53 [INFO] Processing SRX3031098. (1/5)
2021-08-23 13:16:53 [INFO] Processing SRX3031098-SRR5862508. (1/5)
2021-08-23 13:16:57 [INFO] Processing SRX3031096. (2/5)
2021-08-23 13:16:57 [INFO] Processing SRX3031096-SRR5862506. (2/5)
2021-08-23 13:17:03 [INFO] Processing SRX3031099. (3/5)
2021-08-23 13:17:03 [INFO] Processing SRX3031099-SRR5862509. (3/5)
2021-08-23 13:17:07 [INFO] Processing SRX3031097. (4/5)
2021-08-23 13:17:07 [INFO] Processing SRX3031097-SRR5862507. (4/5)
2021-08-23 13:17:12 [INFO] Processing SRX3031100. (5/5)
2021-08-23 13:17:12 [INFO] Processing SRX3031100-SRR5862510. (5/5)
2021-08-23 13:17:17 [INFO] Writing to disk...
2021-08-23 13:17:18 [INFO] Finished.