2021-06-10 04:30:17 [INFO] Starting.
2021-06-10 04:30:17 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/
2021-06-10 04:30:17 [INFO] Creating new aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/aggregate.hdf5
2021-06-10 04:30:17 [INFO] Using chromosome sizes at /grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes
2021-06-10 04:30:17 [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 04:30:18 [INFO] Building aggregate.
2021-06-10 04:30:18 [INFO] Writing every 10 Runs.
2021-06-10 04:30:18 [INFO] Processing SRX3358200. (1/2)
2021-06-10 04:30:18 [INFO] Processing SRX3358200-SRR6251265. (1/2)
2021-06-10 04:30:25 [INFO] Processing SRX3358199. (2/2)
2021-06-10 04:30:25 [INFO] Processing SRX3358199-SRR6251266. (2/2)
2021-06-10 04:30:49 [INFO] Writing to disk...
2021-06-10 04:30:51 [INFO] Finished.
2021-08-02 17:08:55 [INFO] Starting.
2021-08-02 17:08:56 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/
2021-08-02 17:08:56 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/aggregate.hdf5
2021-08-02 17:08:56 [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 SRX3358200. (1/2)
2021-08-02 17:08:56 [INFO] Processing SRX3358200-SRR6251265. (1/2)
2021-08-02 17:28:39 [INFO] Processing SRX3358199. (2/2)
2021-08-02 17:28:39 [INFO] Processing SRX3358199-SRR6251266. (2/2)
2021-08-02 17:31:30 [ERROR] Adding SRR6251266:chr1_vs_chr4 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 950. MiB for an array with shape (248956423,) and data type int32

2021-08-04 22:18:40 [INFO] Starting.
2021-08-04 22:18:40 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/
2021-08-04 22:18:40 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/aggregate.hdf5
2021-08-04 22:18:40 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-04 22:18:40 [INFO] Building aggregate for 1bp_raw network.
2021-08-04 22:18:40 [INFO] Writing every 10 Runs.
2021-08-04 22:18:40 [INFO] Processing SRX3358200. (1/2)
2021-08-04 22:18:40 [INFO] Processing SRX3358200-SRR6251265. (1/2)
2021-08-04 22:23:31 [INFO] Processing SRX3358199. (2/2)
2021-08-04 22:23:31 [INFO] Processing SRX3358199-SRR6251266. (2/2)
2021-08-04 22:31:49 [INFO] Writing to disk...
2021-08-04 22:32:42 [INFO] Finished.
2021-08-12 14:34:56 [INFO] Starting.
2021-08-12 14:34:56 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/
2021-08-12 14:34:56 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/aggregate.hdf5
2021-08-12 14:34:56 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-12 14:34:57 [INFO] Building aggregate for 40kbp_raw network.
2021-08-12 14:34:57 [INFO] Writing every 10 Runs.
2021-08-12 14:34:57 [INFO] Processing SRX3358200. (1/2)
2021-08-12 14:34:57 [INFO] Processing SRX3358200-SRR6251265. (1/2)
2021-08-12 14:35:05 [INFO] Processing SRX3358199. (2/2)
2021-08-12 14:35:05 [INFO] Processing SRX3358199-SRR6251266. (2/2)
2021-08-12 14:35:29 [INFO] Writing to disk...
2021-08-12 14:35:33 [INFO] Finished.
2021-08-12 15:13:14 [INFO] Starting.
2021-08-12 15:13:14 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/
2021-08-12 15:13:14 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/aggregate.hdf5
2021-08-12 15:13:14 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-12 15:13:15 [INFO] Building aggregate for 25kbp_raw network.
2021-08-12 15:13:15 [INFO] Writing every 10 Runs.
2021-08-12 15:13:15 [INFO] Processing SRX3358200. (1/2)
2021-08-12 15:13:15 [INFO] Processing SRX3358200-SRR6251265. (1/2)
2021-08-12 15:13:24 [INFO] Processing SRX3358199. (2/2)
2021-08-12 15:13:24 [INFO] Processing SRX3358199-SRR6251266. (2/2)
2021-08-12 15:13:44 [INFO] Writing to disk...
2021-08-12 15:13:48 [INFO] Finished.
2021-08-12 15:48:23 [INFO] Starting.
2021-08-12 15:48:23 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/
2021-08-12 15:48:23 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/aggregate.hdf5
2021-08-12 15:48:23 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-12 15:48:24 [INFO] Building aggregate for 5kbp_raw network.
2021-08-12 15:48:24 [INFO] Writing every 10 Runs.
2021-08-12 15:48:24 [INFO] Processing SRX3358200. (1/2)
2021-08-12 15:48:24 [INFO] Processing SRX3358200-SRR6251265. (1/2)
2021-08-12 15:48:34 [INFO] Processing SRX3358199. (2/2)
2021-08-12 15:48:34 [INFO] Processing SRX3358199-SRR6251266. (2/2)
2021-08-12 15:49:01 [INFO] Writing to disk...
2021-08-12 15:49:05 [INFO] Finished.
2021-08-12 16:37:17 [INFO] Starting.
2021-08-12 16:37:17 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/
2021-08-12 16:37:17 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/aggregate.hdf5
2021-08-12 16:37:17 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-12 16:37:18 [INFO] Building aggregate for 1kbp_raw network.
2021-08-12 16:37:18 [INFO] Writing every 10 Runs.
2021-08-12 16:37:18 [INFO] Processing SRX3358200. (1/2)
2021-08-12 16:37:18 [INFO] Processing SRX3358200-SRR6251265. (1/2)
2021-08-12 16:37:33 [INFO] Processing SRX3358199. (2/2)
2021-08-12 16:37:33 [INFO] Processing SRX3358199-SRR6251266. (2/2)
2021-08-12 16:38:08 [INFO] Writing to disk...
2021-08-12 16:38:13 [INFO] Finished.
2021-08-20 18:05:35 [INFO] Starting.
2021-08-20 18:05:35 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/
2021-08-20 18:05:35 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/aggregate.hdf5
2021-08-20 18:05:35 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-20 18:05:37 [INFO] Building aggregate for 100kbp_raw network.
2021-08-20 18:05:37 [INFO] Writing every 10 Runs.
2021-08-20 18:05:37 [INFO] Processing SRX3358200. (1/2)
2021-08-20 18:05:37 [INFO] Processing SRX3358200-SRR6251265. (1/2)
2021-08-20 18:05:42 [INFO] Processing SRX3358199. (2/2)
2021-08-20 18:05:42 [INFO] Processing SRX3358199-SRR6251266. (2/2)
2021-08-20 18:05:58 [INFO] Writing to disk...
2021-08-20 18:06:01 [INFO] Finished.
2021-08-23 11:31:42 [INFO] Starting.
2021-08-23 11:31:42 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/
2021-08-23 11:31:42 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/aggregate.hdf5
2021-08-23 11:31:42 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-23 11:31:43 [INFO] Building aggregate for 250kbp_raw network.
2021-08-23 11:31:43 [INFO] Writing every 10 Runs.
2021-08-23 11:31:43 [INFO] Processing SRX3358200. (1/2)
2021-08-23 11:31:43 [INFO] Processing SRX3358200-SRR6251265. (1/2)
2021-08-23 11:31:48 [INFO] Processing SRX3358199. (2/2)
2021-08-23 11:31:48 [INFO] Processing SRX3358199-SRR6251266. (2/2)
2021-08-23 11:31:58 [INFO] Writing to disk...
2021-08-23 11:31:59 [INFO] Finished.
2021-08-23 13:17:33 [INFO] Starting.
2021-08-23 13:17:33 [INFO] Processing /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/
2021-08-23 13:17:33 [INFO] Appending to existing aggregate : /grid/gillis/data/nfox/hi_c_data_processing/data_human/SRP102403/aggregate.hdf5
2021-08-23 13:17:33 [WARNING] chroms=/grid/gillis/data/nfox/genomes/homo_sapiens_38/hg38.chrom.sizes is ignored due to existing aggregate.
2021-08-23 13:17:34 [INFO] Building aggregate for 500kbp_raw network.
2021-08-23 13:17:34 [INFO] Writing every 10 Runs.
2021-08-23 13:17:34 [INFO] Processing SRX3358200. (1/2)
2021-08-23 13:17:34 [INFO] Processing SRX3358200-SRR6251265. (1/2)
2021-08-23 13:17:37 [INFO] Processing SRX3358199. (2/2)
2021-08-23 13:17:37 [INFO] Processing SRX3358199-SRR6251266. (2/2)
2021-08-23 13:17:44 [INFO] Writing to disk...
2021-08-23 13:17:45 [INFO] Finished.