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not found #7

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KMbio43 opened this issue Dec 10, 2021 · 1 comment
Open

not found #7

KMbio43 opened this issue Dec 10, 2021 · 1 comment

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@KMbio43
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KMbio43 commented Dec 10, 2021

Hello, Prof Huang! I'm sorry to disturb you. I have a question to ask you. I have made some errors while installing diceseq, I think I should be installed successfully, but when running the code there is the following error. I'm not sure if it is my python environment or something else, here is my installation method:
conda create -n dicePy2 python=2.7 numpy==1.15.4 scipy==1.1.0 matplotlib==2.2.3 pysam==0.15.2
source activate dicePy2
and false content:
dice-count -a dice_count.gtf -s SRR5582776sorted.bam -o SRR5582776dice.txt --junction
Welcome to dice-count!
loading annotation file... Done.
Traceback (most recent call last):
File "/home/MK/anaconda3/bin/dice-count", line 8, in
sys.exit(main())
File "/home/MK/anaconda3/lib/python3.7/site-packages/diceseq/dice_count.py", line 132, in main
_map_num = np.loadtxt(pysam.idxstats(sam_file), "str")[:,2]
File "/home/MK/anaconda3/lib/python3.7/site-packages/numpy/lib/npyio.py", line 926, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/home/MK/anaconda3/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 262, in open
return ds.open(path, mode, encoding=encoding, newline=newline)
File "/home/MK/anaconda3/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 618, in open
raise IOError("%s not found." % path)
OSError: I 230218 4139798 0
II 813184 16449284 0
III 316620 3758010 0
IV 1531933 19246328 0
V 576874 15693472 0
VI 270161 2536644 0
VII 1090940 18417732 0
VIII 562643 8431090 0
IX 439888 3765040 0
X 745751 10401514 0
XI 666816 8530514 0
XII 1078177 30091252 0
XIII 924431 12279986 0
XIV 784333 8578248 0
XV 1091291 15079578 0
XVI 948066 14969088 0
Mito 85779 928264 0

  • 0 0 0
    not found.
@huangyh09
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Thanks for your question. It looks it still uses Python 3.7.

Before you install DICE-seq, you activated the environment (which you specified as python=2.7), right?

Yuanhua

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