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vaquerizaslab / fanc

FAN-C: Framework for the ANalysis of C-like data
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RuntimeError: Task had non-zero exit status. Cancelling execution of all tasks. #9

Closed Rseq closed 4 years ago

Rseq commented 4 years ago

Hi,

Many thanks for making this toolset available. I'm trying to run fanc compartments on my dataset. If I got it right, I should first convert my Hi-C analysis output into fanc input using fanc auto. Once I do this first step, using .validpairs as fanc auto, I get this error:

$ fanc auto '/media/test/Data/Data/HiC/HiC_fused_150_PE/HiCPro_HiC_fused_150_PE/hic_results/data/K5testEtOH/K5testEtOH.allValidPairs' -g '/media/test/Data/Genomes_ref/bowtie2/Hsapiens/digested_ref/DpnII_resfrag_hg19.bed' '/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC' 
2020-02-17 12:05:43,260 INFO Output folder: /media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/
2020-02-17 12:05:43,260 INFO Input files: /media/test/Data/Data/HiC/HiC_fused_150_PE/HiCPro_HiC_fused_150_PE/hic_results/data/K5testEtOH/K5testEtOH.allValidPairs
2020-02-17 12:05:43,260 INFO Input file types: pairs_txt
2020-02-17 12:05:43,260 INFO Final basename: K5testEtOH (you can change this with the -n option!)
2020-02-17 12:05:43,260 INFO Creating output folders...
2020-02-17 12:05:44,882 INFO Getting genome regions (fragments or bins)
2020-02-17 12:05:44,882 INFO Getting regions
2020-02-17 12:05:44,883 INFO Two arguments detected, assuming HiC-Pro or 4D Nucleome input.
Traceback (most recent call last):
  File "tables/tableextension.pyx", line 1590, in tables.tableextension.Row.__setitem__
TypeError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/fanc", line 124, in <module>
    Fanc()
  File "/usr/local/bin/fanc", line 90, in __init__
    command([sys.argv[0]] + sys.argv[option_ix:], log_level=log_level, verbosity=verbosity)
  File "/usr/local/lib/python3.6/dist-packages/fanc/commands/fanc_commands.py", line 966, in pairs
    pairs.add_regions(regions, preserve_attributes=False)
  File "/usr/local/lib/python3.6/dist-packages/fanc/regions.py", line 664, in add_regions
    self.add_region(region, *args, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/genomic_regions/regions.py", line 1219, in add_region
    return self._add_region(new_region, *args, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/fanc/regions.py", line 602, in _add_region
    row['end'] = region.end
  File "tables/tableextension.pyx", line 1595, in tables.tableextension.Row.__setitem__
TypeError: invalid type (<class 'str'>) for column ``end``
Closing remaining open files:/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/pairs/K5testEtOH_0.pairs...done
Exception ignored in: <object repr() failed>
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/tables/node.py", line 319, in __del__
  File "/usr/local/lib/python3.6/dist-packages/tables/table.py", line 2961, in _f_close
  File "/usr/local/lib/python3.6/dist-packages/tables/table.py", line 2895, in flush
  File "tables/tableextension.pyx", line 1337, in tables.tableextension.Row._flush_buffered_rows
  File "tables/tableextension.pyx", line 752, in tables.tableextension.Row.table.__get__
  File "/usr/local/lib/python3.6/dist-packages/tables/file.py", line 2150, in _check_open
tables.exceptions.ClosedFileError: the file object is closed
Traceback (most recent call last):
  File "/usr/local/bin/fanc", line 124, in <module>
    Fanc()
  File "/usr/local/bin/fanc", line 90, in __init__
    command([sys.argv[0]] + sys.argv[option_ix:], log_level=log_level, verbosity=verbosity)
  File "/usr/local/lib/python3.6/dist-packages/fanc/commands/fanc_commands.py", line 114, in auto
    return fanc.commands.auto.auto(argv, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/fanc/commands/auto.py", line 1181, in auto
    runner.run()
  File "/usr/local/lib/python3.6/dist-packages/fanc/commands/auto.py", line 141, in run
    "Cancelling execution of all tasks.".format(task.id))
RuntimeError: Task 29185059-d866-430e-b45d-3af483602949 had non-zero exit status. Cancelling execution of all tasks.

I'm using Linux, any idea what is going on?

$ python --version
Python 3.6.8
$ fanc --version
0.8.18

thank you for your time,

kaukrise commented 4 years ago

Hi, thank you for the bug report - I encountered this issue myself over the weekend and have already implemented a fix, which will be available shortly. I'll post a comment here when there is a new version!

kaukrise commented 4 years ago

You can upgrade to FAN-C version 0.8.20 now, which should fix the issue you were seeing. Please let me know if you encounter this issue again!

Rseq commented 4 years ago

Hi, thanks for the prompt reply! And for the quick fix!

Does it mean that this is already fixed if I pull in Github or pip should do the trick as well?

A different issue is also preventing me from doing the same using juicebox .hic as input.

kaukrise commented 4 years ago

Both git pull and pip install --upgrade fanc should work. Can you post the Juicer issue separately, so I can have a look, please?

Rseq commented 4 years ago

Hi,

I did as you told and I upgrade it. It is running until a certain point that crashes:

$ fanc auto '/media/test/Data/Data/HiC/HiC_fused_150_PE/HiCPro_HiC_fused_150_PE/hic_results/data/K5_test_EtOH/K5_test_EtOH.allValidPairs' -g '/media/test/Data/Genomes_ref/bowtie2/Hsapiens/digested_ref/DpnII_resfrag_hg19.bed' '/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC' 
2020-02-17 12:47:22,627 INFO Output folder: /media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/
2020-02-17 12:47:22,627 INFO Input files: /media/test/Data/Data/HiC/HiC_fused_150_PE/HiCPro_HiC_fused_150_PE/hic_results/data/K5_test_EtOH/K5_test_EtOH.allValidPairs
2020-02-17 12:47:22,627 INFO Input file types: pairs_txt
2020-02-17 12:47:22,627 INFO Final basename: K5_test_EtOH (you can change this with the -n option!)
2020-02-17 12:47:22,627 INFO Creating output folders...
2020-02-17 12:47:24,188 INFO Getting genome regions (fragments or bins)
2020-02-17 12:47:24,188 INFO Getting regions
2020-02-17 12:47:24,189 INFO Two arguments detected, assuming HiC-Pro or 4D Nucleome input.
2020-02-17 12:58:58,664 INFO Done saving read pairs.
Buffers 100% (5151 of 5151) |##############################################| Elapsed Time: 0:00:30 Time:  0:00:30
2020-02-17 13:02:40,806 INFO Updating region mappability
Mappability 100% (16287066 of 16287066) |##################################| Elapsed Time: 0:01:56 Time:  0:01:56
2020-02-17 13:08:34,968 INFO Done adding pairs.
2020-02-17 13:08:35,087 INFO All done.
2020-02-17 13:08:37,261 INFO One argument received, assuming existing Pairs object.
2020-02-17 13:08:37,297 INFO Filtering reads with RE distance > 10000bp
2020-02-17 13:08:37,297 INFO Filtering self-ligated read pairs
2020-02-17 13:08:37,298 INFO Filtering PCR duplicates, threshold <= 2bp
2020-02-17 13:10:14,797 INFO PCR duplicate stats: 2359 (0.0%) of pairs marked as duplicate.  (multiplicity:occurances) 2:2330 4:3 3:9
2020-02-17 13:10:14,797 INFO Running filters...
Filter 100% (5151 of 5151) |###############################################| Elapsed Time: 0:06:22 Time:  0:06:22
2020-02-17 13:18:00,651 INFO Total: 16287066. Valid: 16284474
2020-02-17 13:18:00,652 INFO Updating region mappability
Mappability 100% (16284474 of 16284474) |##################################| Elapsed Time: 0:01:58 Time:  0:01:58
2020-02-17 13:25:51,568 INFO Done.
2020-02-17 13:27:17,629 INFO Saving statistics...
2020-02-17 13:27:18,721 INFO All done.
2020-02-17 13:27:20,857 INFO One argument received, assuming existing Pairs object.
Ligation error 100% (16287066 of 16287066) |###############################| Elapsed Time: 0:07:26 Time:  0:07:26
2020-02-17 13:38:52,800 INFO Pairs: 16284474
2020-02-17 13:38:52,800 INFO Inter-chromosomal: 4235251
2020-02-17 13:38:52,800 INFO Same fragment: 162
2020-02-17 13:38:52,801 INFO Same: 5945935
2020-02-17 13:38:52,801 INFO Inward: 3146800
2020-02-17 13:38:52,801 INFO Outward: 2953663
2020-02-17 13:40:23,871 INFO All done.
2020-02-17 13:40:25,917 INFO One argument received, assuming existing Pairs object.
2020-02-17 13:42:01,977 INFO All done.
2020-02-17 13:42:04,495 INFO Converting Pairs files
2020-02-17 13:42:04,531 INFO Converting /media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/pairs/K5_test_EtOH_0.pairs to Hic
Hi-C convert 100% (16284474 of 16284474) |#################################| Elapsed Time: 0:04:40 Time:  0:04:40
2020-02-17 13:51:10,722 INFO Binning Hic file (5000000)
2020-02-17 13:51:10,722 INFO Constructing binned genome...
2020-02-17 13:52:06,402 INFO Binning edges...
2020-02-17 13:52:06,474 INFO Binning Hi-C contacts
2020-02-17 13:53:39,849 INFO Launching processes
2020-02-17 13:54:02,484 INFO Submitting partitions
2020-02-17 13:54:02,522 INFO Collecting results
Binning 100% (378 of 378) |################################################| Elapsed Time: 0:51:35 Time:  0:51:35
Buffers 100% (1 of 1) |####################################################| Elapsed Time: 0:00:00 Time:  0:00:00
Expected 100% (191633 of 191633) |#########################################| Elapsed Time: 0:00:16 Time:  0:00:16
2020-02-17 14:46:21,175 INFO Filtering low-coverage bins using absolute cutoff 0.0, relative cutoff 10.0%
2020-02-17 14:46:32,606 INFO Final absolute cutoff threshold is 3.808e+03
2020-02-17 14:46:32,606 INFO Selected a total of 108 (15.4%) regions to be masked
2020-02-17 14:46:32,606 INFO Running filters...
Filter 100% (1 of 1) |#####################################################| Elapsed Time: 0:00:00 Time:  0:00:00
2020-02-17 14:46:38,116 INFO Total: 191633. Filtered: 15159
Expected 100% (176474 of 176474) |#########################################| Elapsed Time: 0:00:14 Time:  0:00:14
2020-02-17 14:46:53,183 INFO Done.
2020-02-17 14:46:53,806 INFO Saving statistics...
2020-02-17 14:46:54,499 INFO Correcting binned Hic file
Expected 100% (176474 of 176474) |#########################################| Elapsed Time: 0:00:15 Time:  0:00:15
Closing remaining open files:/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/hic/K5_test_EtOH_0.hic...done
2020-02-17 14:47:22,256 INFO Binning Hic file (2000000)
2020-02-17 14:47:22,257 INFO Constructing binned genome...
2020-02-17 14:48:19,281 INFO Binning edges...
2020-02-17 14:48:19,370 INFO Binning Hi-C contacts
2020-02-17 14:49:53,093 INFO Launching processes
2020-02-17 14:50:17,138 INFO Submitting partitions
2020-02-17 14:50:17,196 INFO Collecting results
Binning 100% (378 of 378) |################################################| Elapsed Time: 0:50:58 Time:  0:50:58
Buffers 100% (3 of 3) |####################################################| Elapsed Time: 0:00:00 Time:  0:00:00
Expected 100% (986224 of 986224) |#########################################| Elapsed Time: 0:01:27 Time:  0:01:27
2020-02-17 15:43:11,404 INFO Filtering low-coverage bins using absolute cutoff 0.0, relative cutoff 10.0%
2020-02-17 15:44:13,072 INFO Final absolute cutoff threshold is 1.66e+03
2020-02-17 15:44:13,072 INFO Selected a total of 185 (11.3%) regions to be masked
2020-02-17 15:44:13,072 INFO Running filters...
Filter 100% (3 of 3) |#####################################################| Elapsed Time: 0:00:15 Time:  0:00:15
2020-02-17 15:44:40,764 INFO Total: 986224. Filtered: 14200
Expected 100% (972024 of 972024) |#########################################| Elapsed Time: 0:01:24 Time:  0:01:24
2020-02-17 15:46:05,397 INFO Done.
2020-02-17 15:46:05,593 INFO Saving statistics...
2020-02-17 15:46:05,765 INFO Correcting binned Hic file
Expected 100% (972024 of 972024) |#########################################| Elapsed Time: 0:01:24 Time:  0:01:24
Closing remaining open files:/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/hic/K5_test_EtOH_0.hic...done
2020-02-17 15:47:37,969 INFO Binning Hic file (1000000)
2020-02-17 15:47:37,970 INFO Constructing binned genome...
2020-02-17 15:48:33,680 INFO Binning edges...
2020-02-17 15:48:33,801 INFO Binning Hi-C contacts
2020-02-17 15:50:05,273 INFO Launching processes
2020-02-17 15:50:27,625 INFO Submitting partitions
2020-02-17 15:50:27,670 INFO Collecting results
Binning 100% (378 of 378) |################################################| Elapsed Time: 0:52:08 Time:  0:52:08
Buffers 100% (10 of 10) |##################################################| Elapsed Time: 0:00:00 Time:  0:00:00
Expected 100% (2425140 of 2425140) |#######################################| Elapsed Time: 0:03:28 Time:  0:03:28
2020-02-17 16:46:35,777 INFO Filtering low-coverage bins using absolute cutoff 0.0, relative cutoff 10.0%
2020-02-17 16:49:00,944 INFO Final absolute cutoff threshold is 874.6
2020-02-17 16:49:00,945 INFO Selected a total of 336 (10.5%) regions to be masked
2020-02-17 16:49:00,945 INFO Running filters...
Filter 100% (10 of 10) |###################################################| Elapsed Time: 0:00:59 Time:  0:00:59
2020-02-17 16:50:07,847 INFO Total: 2425140. Filtered: 14517
Expected 100% (2410623 of 2410623) |#######################################| Elapsed Time: 0:03:29 Time:  0:03:29
2020-02-17 16:53:37,624 INFO Done.
2020-02-17 16:53:38,317 INFO Saving statistics...
2020-02-17 16:53:38,943 INFO Correcting binned Hic file
Expected 100% (2410623 of 2410623) |#######################################| Elapsed Time: 0:03:28 Time:  0:03:28
Closing remaining open files:/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/hic/K5_test_EtOH_0.hic...done
2020-02-17 16:57:32,753 INFO Binning Hic file (500000)
2020-02-17 16:57:32,753 INFO Constructing binned genome...
2020-02-17 16:58:29,234 INFO Binning edges...
2020-02-17 16:58:29,408 INFO Binning Hi-C contacts
2020-02-17 17:00:04,295 INFO Launching processes
2020-02-17 17:00:27,033 INFO Submitting partitions
2020-02-17 17:00:27,079 INFO Collecting results
Binning 100% (378 of 378) |################################################| Elapsed Time: 0:51:57 Time:  0:51:57
Buffers 100% (28 of 28) |##################################################| Elapsed Time: 0:00:00 Time:  0:00:00
Expected 100% (3976389 of 3976389) |#######################################| Elapsed Time: 0:05:58 Time:  0:05:58
2020-02-17 17:58:57,881 INFO Filtering low-coverage bins using absolute cutoff 0.0, relative cutoff 10.0%
2020-02-17 18:03:06,696 INFO Final absolute cutoff threshold is 458.7
2020-02-17 18:03:06,698 INFO Selected a total of 638 (10.1%) regions to be masked
2020-02-17 18:03:06,698 INFO Running filters...
Filter 100% (28 of 28) |###################################################| Elapsed Time: 0:01:46 Time:  0:01:46
2020-02-17 18:04:59,231 INFO Total: 3976389. Filtered: 12715
Expected 100% (3963674 of 3963674) |#######################################| Elapsed Time: 0:05:49 Time:  0:05:49
2020-02-17 18:10:49,829 INFO Done.
2020-02-17 18:10:50,826 INFO Saving statistics...
2020-02-17 18:10:51,474 INFO Correcting binned Hic file
Expected 100% (3963674 of 3963674) |#######################################| Elapsed Time: 0:05:48 Time:  0:05:48
Closing remaining open files:/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/hic/K5_test_EtOH_0.hic...done
2020-02-17 18:17:34,067 INFO Binning Hic file (250000)
2020-02-17 18:17:34,067 INFO Constructing binned genome...
2020-02-17 18:18:31,528 INFO Binning edges...
2020-02-17 18:18:31,827 INFO Binning Hi-C contacts
2020-02-17 18:20:07,307 INFO Launching processes
2020-02-17 18:20:30,635 INFO Submitting partitions
2020-02-17 18:20:30,688 INFO Collecting results
Binning 100% (378 of 378) |################################################| Elapsed Time: 0:51:49 Time:  0:51:49
Buffers 100% (91 of 91) |##################################################| Elapsed Time: 0:00:00 Time:  0:00:00
Expected 100% (5369691 of 5369691) |#######################################| Elapsed Time: 0:07:43 Time:  0:07:43
2020-02-17 19:20:39,438 INFO Filtering low-coverage bins using absolute cutoff 0.0, relative cutoff 10.0%
2020-02-17 19:25:59,514 INFO Final absolute cutoff threshold is 238.3
2020-02-17 19:25:59,517 INFO Selected a total of 1260 (10.0%) regions to be masked
2020-02-17 19:25:59,517 INFO Running filters...
Filter 100% (91 of 91) |###################################################| Elapsed Time: 0:02:23 Time:  0:02:23
2020-02-17 19:28:28,220 INFO Total: 5369691. Filtered: 12179
Expected 100% (5357512 of 5357512) |#######################################| Elapsed Time: 0:07:45 Time:  0:07:45
2020-02-17 19:36:15,424 INFO Done.
2020-02-17 19:36:16,744 INFO Saving statistics...
2020-02-17 19:36:16,908 INFO Correcting binned Hic file
Expected 100% (5357512 of 5357512) |#######################################| Elapsed Time: 0:07:39 Time:  0:07:39
Closing remaining open files:/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/hic/K5_test_EtOH_0.hic...done
2020-02-17 19:45:36,317 INFO Binning Hic file (100000)
2020-02-17 19:45:36,317 INFO Constructing binned genome...
2020-02-17 19:46:34,006 INFO Binning edges...
2020-02-17 19:46:34,681 INFO Binning Hi-C contacts
2020-02-17 19:48:10,925 INFO Launching processes
2020-02-17 19:48:33,523 INFO Submitting partitions
2020-02-17 19:48:33,584 INFO Collecting results
Binning 100% (378 of 378) |################################################| Elapsed Time: 0:51:51 Time:  0:51:51
Buffers 100% (528 of 528) |################################################| Elapsed Time: 0:00:01 Time:  0:00:01
Expected 100% (7290450 of 7290450) |#######################################| Elapsed Time: 0:10:29 Time:  0:10:29
2020-02-17 20:51:54,939 INFO Filtering low-coverage bins using absolute cutoff 0.0, relative cutoff 10.0%
2020-02-17 20:59:17,808 INFO Final absolute cutoff threshold is 99.1
2020-02-17 20:59:17,815 INFO Selected a total of 3237 (10.3%) regions to be masked
2020-02-17 20:59:17,815 INFO Running filters...
Filter 100% (528 of 528) |#################################################| Elapsed Time: 0:03:28 Time:  0:03:28
2020-02-17 21:02:55,822 INFO Total: 7290450. Filtered: 14365
Expected 100% (7276085 of 7276085) |#######################################| Elapsed Time: 0:10:32 Time:  0:10:32
2020-02-17 21:13:38,361 INFO Done.
2020-02-17 21:13:45,491 INFO Saving statistics...
2020-02-17 21:13:46,176 INFO Correcting binned Hic file
Expected 100% (7276085 of 7276085) |#######################################| Elapsed Time: 0:10:35 Time:  0:10:35
Closing remaining open files:/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/hic/K5_test_EtOH_0.hic...done
2020-02-17 21:28:10,905 INFO Binning Hic file (50000)
2020-02-17 21:28:10,906 INFO Constructing binned genome...
2020-02-17 21:29:08,432 INFO Binning edges...
2020-02-17 21:29:09,842 INFO Binning Hi-C contacts
2020-02-17 21:30:46,173 INFO Launching processes
2020-02-17 21:31:08,439 INFO Submitting partitions
2020-02-17 21:31:08,509 INFO Collecting results
Binning 100% (378 of 378) |################################################| Elapsed Time: 0:51:33 Time:  0:51:33
Buffers 100% (2016 of 2016) |##############################################| Elapsed Time: 0:00:05 Time:  0:00:05
Expected 100% (8857186 of 8857186) |#######################################| Elapsed Time: 0:13:10 Time:  0:13:10
2020-02-17 22:37:56,847 INFO Filtering low-coverage bins using absolute cutoff 0.0, relative cutoff 10.0%
2020-02-17 22:47:12,192 INFO Final absolute cutoff threshold is 50.8
2020-02-17 22:47:12,203 INFO Selected a total of 6583 (10.5%) regions to be masked
2020-02-17 22:47:12,204 INFO Running filters...
Filter 100% (2016 of 2016) |###############################################| Elapsed Time: 0:04:46 Time:  0:04:46
2020-02-17 22:52:24,767 INFO Total: 8857186. Filtered: 15188
Expected 100% (8841998 of 8841998) |#######################################| Elapsed Time: 0:13:12 Time:  0:13:12
2020-02-17 23:06:14,708 INFO Done.
2020-02-17 23:06:40,789 INFO Saving statistics...
2020-02-17 23:06:41,628 INFO Correcting binned Hic file
Expected 100% (8841998 of 8841998) |#######################################| Elapsed Time: 0:13:14 Time:  0:13:14
Closing remaining open files:/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/hic/K5_test_EtOH_0.hic...done
2020-02-17 23:26:17,500 INFO Binning Hic file (25000)
2020-02-17 23:26:17,500 INFO Constructing binned genome...
2020-02-17 23:27:15,896 INFO Binning edges...
2020-02-17 23:27:18,290 INFO Binning Hi-C contacts
2020-02-17 23:28:54,112 INFO Launching processes
2020-02-17 23:29:17,246 INFO Submitting partitions
2020-02-17 23:29:17,349 INFO Collecting results
Binning 100% (378 of 378) |################################################| Elapsed Time: 0:51:30 Time:  0:51:30
Buffers 100% (5151 of 5151) |##############################################| Elapsed Time: 0:00:13 Time:  0:00:13
Expected 100% (10724426 of 10724426) |#####################################| Elapsed Time: 0:16:59 Time:  0:16:59
2020-02-18 00:42:16,957 INFO Filtering low-coverage bins using absolute cutoff 0.0, relative cutoff 10.0%
2020-02-18 00:54:26,081 INFO Final absolute cutoff threshold is 25.9
2020-02-18 00:54:26,102 INFO Selected a total of 13370 (10.7%) regions to be masked
2020-02-18 00:54:26,102 INFO Running filters...
Filter 100% (5151 of 5151) |###############################################| Elapsed Time: 0:06:56 Time:  0:06:56
2020-02-18 01:02:27,412 INFO Total: 10724426. Filtered: 14305
Expected 100% (10710121 of 10710121) |#####################################| Elapsed Time: 0:17:06 Time:  0:17:06
2020-02-18 01:21:27,042 INFO Done.
2020-02-18 01:22:35,330 INFO Saving statistics...
2020-02-18 01:22:36,086 INFO Correcting binned Hic file
Expected 100% (10710121 of 10710121) |#####################################| Elapsed Time: 0:16:59 Time:  0:16:59
Closing remaining open files:/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/hic/K5_test_EtOH_0.hic...done
2020-02-18 01:50:41,601 INFO Binning Hic file (10000)
2020-02-18 01:50:41,601 INFO Constructing binned genome...
2020-02-18 01:51:41,258 INFO Binning edges...
2020-02-18 01:51:47,113 INFO Binning Hi-C contacts
2020-02-18 01:53:26,018 INFO Launching processes
2020-02-18 01:53:48,869 INFO Submitting partitions
2020-02-18 01:53:48,979 INFO Collecting results
Binning 100% (378 of 378) |################################################| Elapsed Time: 0:51:56 Time:  0:51:56
Buffers 100% (5151 of 5151) |##############################################| Elapsed Time: 0:00:15 Time:  0:00:15
Expected 100% (13360813 of 13360813) |#####################################| Elapsed Time: 0:20:38 Time:  0:20:38
2020-02-18 03:11:08,571 INFO Filtering low-coverage bins using absolute cutoff 0.0, relative cutoff 10.0%
2020-02-18 03:25:47,737 INFO Final absolute cutoff threshold is 10.5
2020-02-18 03:25:47,795 INFO Selected a total of 34094 (10.9%) regions to be masked
2020-02-18 03:25:47,795 INFO Running filters...
Filter 100% (5151 of 5151) |###############################################| Elapsed Time: 0:08:07 Time:  0:08:07
2020-02-18 03:35:01,580 INFO Total: 13360813. Filtered: 14492
Expected 100% (13346321 of 13346321) |#####################################| Elapsed Time: 0:20:55 Time:  0:20:55
2020-02-18 04:02:00,309 INFO Done.
2020-02-18 04:03:11,079 INFO Saving statistics...
2020-02-18 04:03:11,884 INFO Correcting binned Hic file
Expected 100% (13346321 of 13346321) |#####################################| Elapsed Time: 0:20:37 Time:  0:20:37
Closing remaining open files:/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/hic/K5_test_EtOH_0.hic...done
2020-02-18 04:56:18,028 INFO Binning Hic file (5000)
2020-02-18 04:56:18,028 INFO Constructing binned genome...
2020-02-18 04:57:22,887 INFO Binning edges...
2020-02-18 04:57:34,575 INFO Binning Hi-C contacts
2020-02-18 04:59:14,861 INFO Launching processes
2020-02-18 04:59:37,658 INFO Submitting partitions
2020-02-18 04:59:37,777 INFO Collecting results
Binning 100% (378 of 378) |################################################| Elapsed Time: 0:51:51 Time:  0:51:51
Buffers 100% (5151 of 5151) |##############################################| Elapsed Time: 0:00:14 Time:  0:00:14
Expected 100% (14872778 of 14872778) |#####################################| Elapsed Time: 0:23:12 Time:  0:23:12
2020-02-18 06:19:41,858 INFO Filtering low-coverage bins using absolute cutoff 0.0, relative cutoff 10.0%
2020-02-18 06:36:20,225 INFO Final absolute cutoff threshold is 5.3
2020-02-18 06:36:20,333 INFO Selected a total of 69835 (11.1%) regions to be masked
2020-02-18 06:36:20,333 INFO Running filters...
Filter 100% (5151 of 5151) |###############################################| Elapsed Time: 0:08:54 Time:  0:08:54
2020-02-18 06:46:20,943 INFO Total: 14872778. Filtered: 16935
Expected 100% (14855843 of 14855843) |#####################################| Elapsed Time: 0:23:16 Time:  0:23:16
2020-02-18 07:30:26,042 INFO Done.
2020-02-18 07:31:34,277 INFO Saving statistics...
2020-02-18 07:31:35,028 INFO Correcting binned Hic file
Traceback (most recent call last):
  File "/usr/local/bin/fanc", line 124, in <module>
    Fanc()
  File "/usr/local/bin/fanc", line 90, in __init__
    command([sys.argv[0]] + sys.argv[option_ix:], log_level=log_level, verbosity=verbosity)
  File "/usr/local/lib/python3.6/dist-packages/fanc/commands/fanc_commands.py", line 1497, in hic
    intra_chromosomal=not only_interchromosomal)
  File "/usr/local/lib/python3.6/dist-packages/fanc/hic.py", line 763, in kr_balancing
    m_corrected, bias_vector_chromosome = correct_matrix(m, restore_coverage=restore_coverage)
  File "/usr/local/lib/python3.6/dist-packages/fanc/hic.py", line 814, in correct_matrix
    m_nonzero = x*m_nonzero*x[:, np.newaxis]
  File "/usr/local/lib/python3.6/dist-packages/numpy/ma/core.py", line 4130, in __mul__
    return multiply(self, other)
  File "/usr/local/lib/python3.6/dist-packages/numpy/ma/core.py", line 1026, in __call__
    result = self.f(da, db, *args, **kwargs)
MemoryError: Unable to allocate 16.5 GiB for an array with shape (47125, 47125) and data type float64
Closing remaining open files:/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/hic/binned/K5_test_EtOH_5kb.hic...done/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC/hic/K5_test_EtOH_0.hic...done
Traceback (most recent call last):
  File "/usr/local/bin/fanc", line 124, in <module>
    Fanc()
  File "/usr/local/bin/fanc", line 90, in __init__
    command([sys.argv[0]] + sys.argv[option_ix:], log_level=log_level, verbosity=verbosity)
  File "/usr/local/lib/python3.6/dist-packages/fanc/commands/fanc_commands.py", line 114, in auto
    return fanc.commands.auto.auto(argv, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/fanc/commands/auto.py", line 1186, in auto
    runner.run()
  File "/usr/local/lib/python3.6/dist-packages/fanc/commands/auto.py", line 141, in run
    "Cancelling execution of all tasks.".format(task.id))
RuntimeError: Task aabf8143-6958-4c0d-9c54-407820d6f987 had non-zero exit status. Cancelling execution of all tasks.

However, it does generate some files - although, not sure if I can use it for further analysis due to the error report

$ tree /media/test/Data/Data/HiC/HiC_fused_150_PE/FANC
/media/test/Data/Data/HiC/HiC_fused_150_PE/FANC
├── fastq
├── hic
│   ├── binned
│   │   ├── K5_test_EtOH_100kb.hic
│   │   ├── K5_test_EtOH_10kb.hic
│   │   ├── K5_test_EtOH_1mb.hic
│   │   ├── K5_test_EtOH_250kb.hic
│   │   ├── K5_test_EtOH_25kb.hic
│   │   ├── K5_test_EtOH_2mb.hic
│   │   ├── K5_test_EtOH_500kb.hic
│   │   ├── K5_test_EtOH_50kb.hic
│   │   ├── K5_test_EtOH_5kb.hic
│   │   └── K5_test_EtOH_5mb.hic
│   └── K5_test_EtOH_0.hic
├── pairs
│   └── K5_test_EtOH_0.pairs
├── plots
│   └── stats
│       ├── K5_test_EtOH_0.pairs.ligation_error.pdf
│       ├── K5_test_EtOH_0.pairs.re_dist.pdf
│       ├── K5_test_EtOH_0.pairs.stats.pdf
│       ├── K5_test_EtOH_100kb.stats.pdf
│       ├── K5_test_EtOH_10kb.stats.pdf
│       ├── K5_test_EtOH_1mb.stats.pdf
│       ├── K5_test_EtOH_250kb.stats.pdf
│       ├── K5_test_EtOH_25kb.stats.pdf
│       ├── K5_test_EtOH_2mb.stats.pdf
│       ├── K5_test_EtOH_500kb.stats.pdf
│       ├── K5_test_EtOH_50kb.stats.pdf
│       ├── K5_test_EtOH_5kb.stats.pdf
│       └── K5_test_EtOH_5mb.stats.pdf
└── sam

7 directories, 25 files
kaukrise commented 4 years ago

Hi, your system is running our of memory. Knight-Ruiz normalisation (the default) works on full numpy matrices, which are loaded on a per-chromosome basis. You can see that the tool is trying and failing to allocate memory here:

MemoryError: Unable to allocate 16.5 GiB for an array with shape (47125, 47125) and data type float64

You can try ICE normalisation instead, which is slower but much more memory-efficient. There is no need to repeat the whole process, you can start from the Hi-C files. For each of your files, simply do:

fanc hic -i <hic_file>

For example

fanc hic -i K5_test_EtOH_1mb.hic
kaukrise commented 4 years ago

Actually, from your logs it seems as though all Hi-C files other than the 5kb binned one are fine, so there is no need to renormalise those

Rseq commented 4 years ago

Many thanks for your input. Maybe it is related to the fact that is not sequenced deeper enough to analyse at 5 kb.. As I think 500gb RAM memory should not be a limiting factor. Closing here! thanks!

kaukrise commented 4 years ago

It looks as though the 500Gb are not available to the process running FAN-C, though, so you might want to check system limits. I am successfully running KR matrix normalisation on machines with a lot less memory (32Gb). The memory error is generated by Numpy, which can't allocate 16Gb - so either some other process is using up all the memory or there is some limit on memory available per process.