2021-06-10 03:57:30 [INFO] Starting.
2021-06-10 03:57:30 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/
2021-06-10 03:57:30 [INFO] Creating new aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/aggregate.hdf5
2021-06-10 03:57:30 [INFO] Using chromosome sizes at /grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes
2021-06-10 03:57:30 [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 03:57:31 [INFO] Building aggregate.
2021-06-10 03:57:31 [INFO] Writing every 10 Runs.
2021-06-10 03:57:31 [INFO] Processing SRX4659094. (1/4)
2021-06-10 03:57:31 [INFO] Processing SRX4659094-SRR7807397. (1/6)
2021-06-10 03:57:42 [INFO] Processing SRX4659096. (2/4)
2021-06-10 03:57:42 [INFO] Processing SRX4659096-SRR7807400. (2/6)
2021-06-10 03:57:54 [INFO] Processing SRX4659096-SRR7807399. (3/6)
2021-06-10 03:58:07 [INFO] Processing SRX4659097. (3/4)
2021-06-10 03:58:07 [INFO] Processing SRX4659097-SRR7807402. (4/6)
2021-06-10 03:58:18 [INFO] Processing SRX4659097-SRR7807401. (5/6)
2021-06-10 03:58:26 [INFO] Processing SRX4659095. (4/4)
2021-06-10 03:58:26 [INFO] Processing SRX4659095-SRR7807398. (6/6)
2021-06-10 03:58:49 [INFO] Writing to disk...
2021-06-10 03:58:53 [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/SRP145420/
2021-08-02 17:08:55 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/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 SRX4659094. (1/4)
2021-08-02 17:08:56 [INFO] Processing SRX4659094-SRR7807397. (1/6)
2021-08-02 17:39:34 [INFO] Processing SRX4659096. (2/4)
2021-08-02 17:39:34 [INFO] Processing SRX4659096-SRR7807400. (2/6)
2021-08-02 17:50:49 [ERROR] Adding SRR7807400:chr7_vs_chr9 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 608. MiB for an array with shape (159345974,) and data type int32

2021-08-04 22:06:55 [INFO] Starting.
2021-08-04 22:06:55 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/
2021-08-04 22:06:55 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/aggregate.hdf5
2021-08-04 22:06:55 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-04 22:06:56 [INFO] Building aggregate for 1bp_raw network.
2021-08-04 22:06:56 [INFO] Writing every 10 Runs.
2021-08-04 22:06:56 [INFO] Processing SRX4659094. (1/4)
2021-08-04 22:06:56 [INFO] Processing SRX4659094-SRR7807397. (1/6)
2021-08-04 22:10:24 [INFO] Processing SRX4659096. (2/4)
2021-08-04 22:10:24 [INFO] Processing SRX4659096-SRR7807400. (2/6)
2021-08-04 22:17:58 [INFO] Processing SRX4659096-SRR7807399. (3/6)
2021-08-04 22:25:22 [INFO] Processing SRX4659097. (3/4)
2021-08-04 22:25:23 [INFO] Processing SRX4659097-SRR7807402. (4/6)
2021-08-04 22:32:50 [INFO] Processing SRX4659097-SRR7807401. (5/6)
2021-08-04 22:40:34 [INFO] Processing SRX4659095. (4/4)
2021-08-04 22:40:34 [INFO] Processing SRX4659095-SRR7807398. (6/6)
2021-08-04 22:47:58 [INFO] Writing to disk...
2021-08-04 22:48:41 [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/SRP145420/
2021-08-12 14:31:17 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/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 SRX4659094. (1/4)
2021-08-12 14:31:18 [INFO] Processing SRX4659094-SRR7807397. (1/6)
2021-08-12 14:31:30 [INFO] Processing SRX4659096. (2/4)
2021-08-12 14:31:30 [INFO] Processing SRX4659096-SRR7807400. (2/6)
2021-08-12 14:31:43 [INFO] Processing SRX4659096-SRR7807399. (3/6)
2021-08-12 14:31:54 [INFO] Processing SRX4659097. (3/4)
2021-08-12 14:31:54 [INFO] Processing SRX4659097-SRR7807402. (4/6)
2021-08-12 14:32:06 [INFO] Processing SRX4659097-SRR7807401. (5/6)
2021-08-12 14:32:16 [INFO] Processing SRX4659095. (4/4)
2021-08-12 14:32:16 [INFO] Processing SRX4659095-SRR7807398. (6/6)
2021-08-12 14:32:28 [INFO] Writing to disk...
2021-08-12 14:32:32 [INFO] Finished.
2021-08-12 15:09:39 [INFO] Starting.
2021-08-12 15:09:39 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/
2021-08-12 15:09:39 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/aggregate.hdf5
2021-08-12 15:09:39 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-12 15:09:40 [INFO] Building aggregate for 25kbp_raw network.
2021-08-12 15:09:40 [INFO] Writing every 10 Runs.
2021-08-12 15:09:40 [INFO] Processing SRX4659094. (1/4)
2021-08-12 15:09:40 [INFO] Processing SRX4659094-SRR7807397. (1/6)
2021-08-12 15:09:52 [INFO] Processing SRX4659096. (2/4)
2021-08-12 15:09:52 [INFO] Processing SRX4659096-SRR7807400. (2/6)
2021-08-12 15:10:04 [INFO] Processing SRX4659096-SRR7807399. (3/6)
2021-08-12 15:10:17 [INFO] Processing SRX4659097. (3/4)
2021-08-12 15:10:17 [INFO] Processing SRX4659097-SRR7807402. (4/6)
2021-08-12 15:10:26 [INFO] Processing SRX4659097-SRR7807401. (5/6)
2021-08-12 15:10:36 [INFO] Processing SRX4659095. (4/4)
2021-08-12 15:10:36 [INFO] Processing SRX4659095-SRR7807398. (6/6)
2021-08-12 15:10:49 [INFO] Writing to disk...
2021-08-12 15:10:52 [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/SRP145420/
2021-08-12 15:44:39 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/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 SRX4659094. (1/4)
2021-08-12 15:44:40 [INFO] Processing SRX4659094-SRR7807397. (1/6)
2021-08-12 15:44:55 [INFO] Processing SRX4659096. (2/4)
2021-08-12 15:44:55 [INFO] Processing SRX4659096-SRR7807400. (2/6)
2021-08-12 15:45:09 [INFO] Processing SRX4659096-SRR7807399. (3/6)
2021-08-12 15:45:23 [INFO] Processing SRX4659097. (3/4)
2021-08-12 15:45:23 [INFO] Processing SRX4659097-SRR7807402. (4/6)
2021-08-12 15:45:33 [INFO] Processing SRX4659097-SRR7807401. (5/6)
2021-08-12 15:45:43 [INFO] Processing SRX4659095. (4/4)
2021-08-12 15:45:43 [INFO] Processing SRX4659095-SRR7807398. (6/6)
2021-08-12 15:45:58 [INFO] Writing to disk...
2021-08-12 15:46:03 [INFO] Finished.
2021-08-12 16:32:23 [INFO] Starting.
2021-08-12 16:32:23 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/
2021-08-12 16:32:23 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/aggregate.hdf5
2021-08-12 16:32:23 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-12 16:32:24 [INFO] Building aggregate for 1kbp_raw network.
2021-08-12 16:32:24 [INFO] Writing every 10 Runs.
2021-08-12 16:32:24 [INFO] Processing SRX4659094. (1/4)
2021-08-12 16:32:24 [INFO] Processing SRX4659094-SRR7807397. (1/6)
2021-08-12 16:32:36 [INFO] Processing SRX4659096. (2/4)
2021-08-12 16:32:36 [INFO] Processing SRX4659096-SRR7807400. (2/6)
2021-08-12 16:32:50 [INFO] Processing SRX4659096-SRR7807399. (3/6)
2021-08-12 16:33:05 [INFO] Processing SRX4659097. (3/4)
2021-08-12 16:33:05 [INFO] Processing SRX4659097-SRR7807402. (4/6)
2021-08-12 16:33:16 [INFO] Processing SRX4659097-SRR7807401. (5/6)
2021-08-12 16:33:27 [INFO] Processing SRX4659095. (4/4)
2021-08-12 16:33:27 [INFO] Processing SRX4659095-SRR7807398. (6/6)
2021-08-12 16:33:42 [INFO] Writing to disk...
2021-08-12 16:33:47 [INFO] Finished.
2021-08-20 17:58:56 [INFO] Starting.
2021-08-20 17:58:56 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/
2021-08-20 17:58:56 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/aggregate.hdf5
2021-08-20 17:58:56 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-20 17:58:57 [INFO] Building aggregate for 100kbp_raw network.
2021-08-20 17:58:57 [INFO] Writing every 10 Runs.
2021-08-20 17:58:57 [INFO] Processing SRX4659094. (1/4)
2021-08-20 17:58:57 [INFO] Processing SRX4659094-SRR7807397. (1/6)
2021-08-20 17:59:07 [INFO] Processing SRX4659096. (2/4)
2021-08-20 17:59:07 [INFO] Processing SRX4659096-SRR7807400. (2/6)
2021-08-20 17:59:15 [INFO] Processing SRX4659096-SRR7807399. (3/6)
2021-08-20 17:59:25 [INFO] Processing SRX4659097. (3/4)
2021-08-20 17:59:25 [INFO] Processing SRX4659097-SRR7807402. (4/6)
2021-08-20 17:59:31 [INFO] Processing SRX4659097-SRR7807401. (5/6)
2021-08-20 17:59:38 [INFO] Processing SRX4659095. (4/4)
2021-08-20 17:59:38 [INFO] Processing SRX4659095-SRR7807398. (6/6)
2021-08-20 17:59:49 [INFO] Writing to disk...
2021-08-20 17:59:50 [INFO] Finished.
2021-08-23 11:30:08 [INFO] Starting.
2021-08-23 11:30:08 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/
2021-08-23 11:30:08 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/aggregate.hdf5
2021-08-23 11:30:08 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-23 11:30:09 [INFO] Building aggregate for 250kbp_raw network.
2021-08-23 11:30:09 [INFO] Writing every 10 Runs.
2021-08-23 11:30:09 [INFO] Processing SRX4659094. (1/4)
2021-08-23 11:30:09 [INFO] Processing SRX4659094-SRR7807397. (1/6)
2021-08-23 11:30:15 [INFO] Processing SRX4659096. (2/4)
2021-08-23 11:30:15 [INFO] Processing SRX4659096-SRR7807400. (2/6)
2021-08-23 11:30:22 [INFO] Processing SRX4659096-SRR7807399. (3/6)
2021-08-23 11:30:27 [INFO] Processing SRX4659097. (3/4)
2021-08-23 11:30:27 [INFO] Processing SRX4659097-SRR7807402. (4/6)
2021-08-23 11:30:33 [INFO] Processing SRX4659097-SRR7807401. (5/6)
2021-08-23 11:30:38 [INFO] Processing SRX4659095. (4/4)
2021-08-23 11:30:38 [INFO] Processing SRX4659095-SRR7807398. (6/6)
2021-08-23 11:30:44 [INFO] Writing to disk...
2021-08-23 11:30:45 [INFO] Finished.
2021-08-23 13:16:44 [INFO] Starting.
2021-08-23 13:16:44 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/
2021-08-23 13:16:44 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP145420/aggregate.hdf5
2021-08-23 13:16:44 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-23 13:16:45 [INFO] Building aggregate for 500kbp_raw network.
2021-08-23 13:16:45 [INFO] Writing every 10 Runs.
2021-08-23 13:16:45 [INFO] Processing SRX4659094. (1/4)
2021-08-23 13:16:45 [INFO] Processing SRX4659094-SRR7807397. (1/6)
2021-08-23 13:16:50 [INFO] Processing SRX4659096. (2/4)
2021-08-23 13:16:50 [INFO] Processing SRX4659096-SRR7807400. (2/6)
2021-08-23 13:16:54 [INFO] Processing SRX4659096-SRR7807399. (3/6)
2021-08-23 13:16:59 [INFO] Processing SRX4659097. (3/4)
2021-08-23 13:16:59 [INFO] Processing SRX4659097-SRR7807402. (4/6)
2021-08-23 13:17:02 [INFO] Processing SRX4659097-SRR7807401. (5/6)
2021-08-23 13:17:05 [INFO] Processing SRX4659095. (4/4)
2021-08-23 13:17:05 [INFO] Processing SRX4659095-SRR7807398. (6/6)
2021-08-23 13:17:10 [INFO] Writing to disk...
2021-08-23 13:17:10 [INFO] Finished.