AttributeError: module 'numpy' has no attribute 'object'

[timothykoala]

Hi Dr. Wang,
I tried to convert a hg19 .hic into hg38 .hic by command line below and faced an error:

pairLiftOver --input /RPE-1_HiC/GSE71831_RPE1-WT.hic --input-format juicer --out-pre test-hg38 --output-format hic --out-chromsizes hg38.chrom.sizes --in-assembly hg19 --out-assembly hg38 --logFile pairLiftOver.log --memory 14G

Here is the log:

# ARGUMENT LIST:
# Input path = /RPE-1_HiC/GSE71831_RPE1-WT.hic
# Input format = juicer
# Output prefix = test-hg38
# Output format = hic
# Chromosome Sizes of the output assembly = hg38.chrom.sizes
# Generate contact maps at 11 resolutions = False
# Input assembly = hg19
# Output assembly = hg38
# Chain file = None
# Temporary Dir = .pairliftover
# Allocated memory = 14G
# Number of Processes = 8
# Log file name = /RPE-1_HiC/pairLiftOver.log
/home/txpn/anaconda3/envs/pairliftover/lib/python3.9/site-packages/cooler/util.py:690: FutureWarning: In the future `np.object` will be defined as the corresponding NumPy scalar.  (This may have returned Python scalars in past versions.
  columns, dtype=None, index_columns=None, index_names=None, default_dtype=np.object
Traceback (most recent call last):
  File "/home/txpn/anaconda3/envs/pairliftover/bin/pairLiftOver", line 137, in <module>
    run()
  File "/home/txpn/anaconda3/envs/pairliftover/bin/pairLiftOver", line 101, in run
    from pairLiftOver.utilities import liftover
  File "/home/txpn/anaconda3/envs/pairliftover/lib/python3.9/site-packages/pairLiftOver/utilities.py", line 1, in <module>
    import subprocess, sys, os, io, logging, cooler, pairLiftOver
  File "/home/txpn/anaconda3/envs/pairliftover/lib/python3.9/site-packages/cooler/__init__.py", line 14, in <module>
    from .api import Cooler, annotate
  File "/home/txpn/anaconda3/envs/pairliftover/lib/python3.9/site-packages/cooler/api.py", line 22, in <module>
    from .util import parse_cooler_uri, parse_region, open_hdf5, closing_hdf5
  File "/home/txpn/anaconda3/envs/pairliftover/lib/python3.9/site-packages/cooler/util.py", line 690, in <module>
    columns, dtype=None, index_columns=None, index_names=None, default_dtype=np.object
  File "/home/txpn/anaconda3/envs/pairliftover/lib/python3.9/site-packages/numpy/__init__.py", line 284, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'object'

Thanks in advance for developing the tool and looking forward for more discussion.

Sincerely,
Timothy

[timothykoala]

Update: Looks like the solution is downgrade numpy.

python -m pip uninstall numpy
python -m pip install numpy==1.23.1

Will provide an update for the result.

[timothykoala]

Preprocess done, suggested downgrade numpy solved the problem.
I got two errors on the following process: OutOfMemoryError and CalledProcessError, but I still got a functional hg38.hic at outpuit. Maybe I need to allocate more memory next time?

Calculating norms for zoom BP_2500000 Calculating norms for zoom BP_1000000 Calculating norms for zoom BP_500000 Calculating norms for zoom BP_250000 Calculating norms for zoom BP_100000 Calculating norms for zoom BP_50000 Calculating norms for zoom BP_25000Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.base/java.util.Arrays.copyOf(Arrays.java:3481) at java.base/java.util.ArrayList.grow(ArrayList.java:237) at java.base/java.util.ArrayList.grow(ArrayList.java:244) at java.base/java.util.ArrayList.add(ArrayList.java:454) at java.base/java.util.ArrayList.add(ArrayList.java:467) at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.createWholeGenomeRecords(GenomeWideNormalizationVectorUpdater.java:207) at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.getWGVectors(GenomeWideNormalizationVectorUpdater.java:134) at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.updateHicFileForGWfromPreOnly(GenomeWideNormalizationVectorUpdater.java:226) at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:76) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:127) at juicebox.tools.HiCTools.main(HiCTools.java:96) Traceback (most recent call last): File "/home/txpn/anaconda3/envs/pairliftover/bin/pairLiftOver", line 137, in <module> run() File "/home/txpn/anaconda3/envs/pairliftover/bin/pairLiftOver", line 123, in run liftover( File "/home/txpn/anaconda3/envs/pairliftover/lib/python3.9/site-packages/pairLiftOver/utilities.py", line 253, in liftover subprocess.check_call(' '.join(command), shell=True) File "/home/txpn/anaconda3/envs/pairliftover/lib/python3.9/subprocess.py", line 373, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'java -Xmx15g -jar /home/txpn/anaconda3/envs/pairliftover/lib/python3.9/site-packages/pairLiftOver/data/juicer_tools_1.11.09_jcuda.0.8.jar pre -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000 /home/txpn/.pairliftover/test-hg38.pairs.gz test-hg38.hic hg38.chrom.sizes' returned non-zero exit status 1.

[XiaoTaoWang]

Thanks for your feedback! Yes, --output-format hic generally need more memory to be allocated.

[timothykoala]

changed to --memory 40G, The conversion done perfectly.
Thanks for developing the tool!