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MGI-tech-bioinformatics / DNBelab_C_Series_HT_scRNA-analysis-software

An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets
MIT License
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DNBC4tools主程序报错 #16

Closed gogozyz closed 2 months ago

gogozyz commented 1 year ago

感谢团队辛苦工作和付出。 目前遇到一主程序报错，烦请帮忙分析解决，报错代码如下： 2023-03-03 11:13:07,903 - count - INFO - Promgram start... 2023-03-03 11:13:07,903 - count - INFO - /home/gogozyz/anaconda3/envs/DNBC4tools/bin/python /home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/rna/cellMerge.py --indir /home/gogozyz/storagezyz/scRNA-seq/test/02.count --name test Traceback (most recent call last): File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/rna/cellMerge.py", line 103, in from plotnine import * File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/init.py", line 1, in from .qplot import qplot # noqa: F401 File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/qplot.py", line 9, in from .ggplot import ggplot File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/ggplot.py", line 20, in from .facets import facet_null File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/facets/init.py", line 1, in from .facet_grid import facet_grid File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/facets/facet_grid.py", line 6, in from .facet import facet, layout_null, combine_vars, add_missing_facets File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/facets/facet.py", line 13, in from ..scales.scales import Scales File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/scales/init.py", line 83, in from .limits import xlim, ylim, lims, expand_limits File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/scales/limits.py", line 8, in from ..geoms import geom_blank File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/geoms/init.py", line 6, in from .geom_abline import geom_abline File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/geoms/geom_abline.py", line 9, in from .geom import geom File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/geoms/geom.py", line 3, in from ..stats.stat import stat File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/stats/init.py", line 6, in from .stat_density import stat_density File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/plotnine/stats/stat_density.py", line 6, in import statsmodels.api as sm File "/home/gogozyz/.local/lib/python3.8/site-packages/statsmodels/api.py", line 123, in from .tsa import api as tsa File "/home/gogozyz/.local/lib/python3.8/site-packages/statsmodels/tsa/api.py", line 74, in from .filters import api as filters, bk_filter, cf_filter, hp_filter File "/home/gogozyz/.local/lib/python3.8/site-packages/statsmodels/tsa/filters/api.py", line 6, in from .filtertools import miso_lfilter, convolution_filter, recursive_filter File "/home/gogozyz/.local/lib/python3.8/site-packages/statsmodels/tsa/filters/filtertools.py", line 18, in from scipy.signal.signaltools import _centered as trim_centered ImportError: cannot import name '_centered' from 'scipy.signal.signaltools' (/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/scipy/signal/signaltools.py) Traceback (most recent call last): File "/home/gogozyz/anaconda3/envs/DNBC4tools/bin/DNBC4tools", line 8, in sys.exit(main()) File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/DNBC4tools.py", line 43, in main args.func(args) File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/count.py", line 71, in count Count(args).run() File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/count.py", line 59, in run logging_call(CellMerge_cmd,'count',self.outdir) File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/utils.py", line 50, in logging_call check_call(popenargs,shell=True) File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/home/gogozyz/anaconda3/envs/DNBC4tools/bin/python /home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/rna/cellMerge.py --indir /home/gogozyz/storagezyz/scRNA-seq/test/02.count --name test' returned non-zero exit status 1. Traceback (most recent call last): File "/home/gogozyz/anaconda3/envs/DNBC4tools/bin/DNBC4tools", line 8, in sys.exit(main()) File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/DNBC4tools.py", line 43, in main args.func(args) File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/run.py", line 78, in run Runpipe(args).runpipe() File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/run.py", line 70, in runpipe start_print_cmd(pipecmd) File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/utils.py", line 31, in start_print_cmd check_call(arg,shell=True) File "/home/gogozyz/anaconda3/envs/DNBC4tools/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'DNBC4tools count --name test --raw_matrix /home/gogozyz/storagezyz/scRNA-seq/test/01.data/raw_matrix --bam /home/gogozyz/storagezyz/scRNA-seq/test/01.data/final_sorted.bam --calling_method emptydrops --expectcells 10000 --forcecells 0 --minumi 1000 --cDNAbarcodeCount /home/gogozyz/storagezyz/scRNA-seq/test/01.data/cDNA_barcode_counts_raw.txt --Indexreads /home/gogozyz/storagezyz/scRNA-seq/test/01.data/Index_reads.fq.gz --oligobarcodeCount /home/gogozyz/storagezyz/scRNA-seq/test/01.data/Index_barcode_counts_raw.txt --thread 24 --outdir /home/gogozyz/storagezyz/scRNA-seq' returned non-zero exit status 1.

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lishuangshuang0616 commented 1 year ago
1677908668478

Thanks for your trust and support. Judging from the error report, it seems that the process caused by your bashrc configuration uses local python package that is not in the DNBC4tools environment. You can first use 

export PATH=/miniconda3/envs/DNBC4tools/bin:$PATH
export LD_LIBRARY_PATH=/miniconda3/envs/DNBC4tools/lib:$LD_LIBRARY_PATH,

because your 01.data has been completed, add --process count,analysis,report to the command line to skip the data step @gogozyz