NameError: name 'pp' is not defined

[mushroomOK]

Hi, I got an error about "NameError: name 'pp' is not defined".
My command: "centromics -p 128 -l $hifi -g V127_CBMhap1.fasta -pre V127_CBMhap1-hifi_hifi -hic ./juicer/aligned/merged_nodups.txt"

"###STDOUT:<< >>
###STDERR:<< Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit
at java.util.Arrays.copyOf(Arrays.java:3236)
at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:118)
at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:135)
at htsjdk.tribble.util.LittleEndianInputStream.readString(LittleEndianInputStream.java:121)
at juicebox.data.DatasetReaderV2.getMagicString(DatasetReaderV2.java:111)
at juicebox.data.HiCFileTools.extractDatasetForCLT(HiCFileTools.java:57)
at juicebox.tools.clt.old.Dump.readArguments(Dump.java:353)
at juicebox.tools.HiCTools.main(HiCTools.java:85)

Traceback (most recent call last):
File "/home/wangj/miniconda3/envs/RepCent/bin/centromics", line 33, in
sys.exit(load_entry_point('Centromics==0.3', 'console_scripts', 'centromics')())
File "/home/wangj/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/pipe.py", line 272, in main
pipeline.run()
File "/home/wangj/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/pipe.py", line 120, in run
hic_bed = self.run_hic()
File "/home/wangj/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/pipe.py", line 254, in run_hic
out1, out2 = count_obs(self.hic, chrLst=self.d_seqL.keys(), prefix=hic_count, tmpdir=tmpdir,
File "/home/wangj/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/Hic.py", line 17, in count_obs
hic2signals(fout1, fout2,
File "/home/wangj/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/Juicer.py", line 97, in hic2signals
d_files = hic2matrix(res=res, **kargs)
File "/home/wangj/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/Juicer.py", line 90, in hic2matrix
d_files = run_juicerbox(inHic, chr_combs, outdir=outdir, res=res, norm=norm, cmd_opts=cmd_opts)
File "/home/wangj/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/Juicer.py", line 23, in run_juicerbox
run_job(cmd_file, cmd_list=cmds, **cmd_opts)
File "/home/wangj/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/RunCmdsMP.py", line 533, in run_job
exit = run_tasks(cmd_list, tc_tasks=tc_tasks, mode=mode, grid_opts=grid_opts,
File "/home/wangj/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/RunCmdsMP.py", line 189, in run_tasks
job_status = pp_run(cmd_list, processors=tc_tasks)
File "/home/wangj/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/RunCmdsMP.py", line 322, in pp_run
job_server = pp.Server(processors, ppservers=ppservers)
NameError: name 'pp' is not defined"

The file of "slurm-2527306_127.txt" includes the whole working log. If you need more information, please let me know. Thanks!
hs_err_pid244723.log
slurm-2527306_127.txt

[zhangrengang]

I sorry that you need to install pp module via conda install pp. I will update the yaml file soon.