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XWangLabTHU / cfDNApipe

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
https://xwanglabthu.github.io/cfDNApipe/
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commonError: Error occured in multi-core running! #11

Closed liujilei156231 closed 9 months ago

liujilei156231 commented 1 year ago 
In [6]: pipeConfigure(
   ...:     threads=1,
   ...:     genome="hg38",
   ...:     refdir="/media/usb2/ref",
   ...:     outdir=r"./fastq/out",
   ...:     data="WGBS",
   ...:     type="paired",
   ...:     build=False,
   ...:     JavaMem="10g",
   ...: )
Background reference check finished!

In [7]: 

In [7]: res = cfDNAWGBS(inputFolder="./fastq/",
   ...:                 idAdapter=False,
   ...:                 rmAdapter=False,
   ...:                 dudup=True,
   ...:                 CNV=True,
   ...:                 armCNV=True,
   ...:                 fragProfile=True,
   ...:                 report=True,
   ...:                 verbose=False)

                                                     #                  #  #                      
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 #   # #   #  #        #   #   #             #    #  #  ##   #  #    #  #  #  ##   #  #    #      
  #  # #  #   #        #####    #####        #    #  #  #    #  #    #  #  #  #    #  #    #      
  # #   # #   #   ###  #    #        #       #####   #  #    #  ######  #  #  #    #  ######      
  # #   # #   #     #  #    #        #       #       #  #    #  #       #  #  #    #  #           
   #     #     #    #  #    #  #     #       #       #  #    #  #    #  #  #  #    #  #    #      
   #     #      #####  #####    #####        #       #  #####    ####   #  #  #    #   ####       
                                                        #                                         
                                                        #                                         
                                                        #                                         

Now, running cell free DNA WGBS data processing pipeline.

paired data is processing......
************************************************************
              inputprocess has been completed!              
************************************************************
Start multicore running, master process number: 1
Note: some command line verbose may be blocked, the program will record them in record file.
Subprocesses Start running......
Waiting for all subprocesses done...
fastqc --outdir /home/liujilei/fastq/out/intermediate_result/step_02_fastqc --threads 1  /home/liujilei/fastq/.ipynb_checkpoints /home/liujilei/fastq/SRR23279758_2.fastq.gz /home/liujilei/fastq/SRR23279758_1.fastq.gz /home/liujilei/fastq/out
All subprocesses done.

^^^

An Error Occured During The Following Command Line Executing.
^^^
fastqc --outdir /home/liujilei/fastq/out/intermediate_result/step_02_fastqc --threads 1  /home/liujilei/fastq/.ipynb_checkpoints /home/liujilei/fastq/SRR23279758_2.fastq.gz /home/liujilei/fastq/SRR23279758_1.fastq.gz /home/liujilei/fastq/out^^^
Failed to process /home/liujilei/fastq/.ipynb_checkpoints
java.io.FileNotFoundException: /home/liujilei/fastq/.ipynb_checkpoints (Is a directory)
        at java.io.FileInputStream.open0(Native Method)
        at java.io.FileInputStream.open(FileInputStream.java:195)
        at java.io.FileInputStream.<init>(FileInputStream.java:138)
        at uk.ac.babraham.FastQC.Sequence.FastQFile.<init>(FastQFile.java:73)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:106)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:159)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:121)
        at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
Started analysis of SRR23279758_2.fastq.gz
Failed to process /home/liujilei/fastq/out
java.io.FileNotFoundException: /home/liujilei/fastq/out (Is a directory)
        at java.io.FileInputStream.open0(Native Method)
        at java.io.FileInputStream.open(FileInputStream.java:195)
        at java.io.FileInputStream.<init>(FileInputStream.java:138)
        at uk.ac.babraham.FastQC.Sequence.FastQFile.<init>(FastQFile.java:73)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:106)
        at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:159)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:121)
        at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
Approx 5% complete for SRR23279758_2.fastq.gz
Approx 10% complete for SRR23279758_2.fastq.gz
Approx 15% complete for SRR23279758_2.fastq.gz
Approx 20% complete for SRR23279758_2.fastq.gz
Approx 25% complete for SRR23279758_2.fastq.gz
Approx 30% complete for SRR23279758_2.fastq.gz
Approx 35% complete for SRR23279758_2.fastq.gz
Approx 40% complete for SRR23279758_2.fastq.gz
Approx 45% complete for SRR23279758_2.fastq.gz
Approx 50% complete for SRR23279758_2.fastq.gz
Approx 55% complete for SRR23279758_2.fastq.gz
Approx 60% complete for SRR23279758_2.fastq.gz
Approx 65% complete for SRR23279758_2.fastq.gz
Approx 70% complete for SRR23279758_2.fastq.gz
Approx 75% complete for SRR23279758_2.fastq.gz
Approx 80% complete for SRR23279758_2.fastq.gz
Approx 85% complete for SRR23279758_2.fastq.gz
Approx 90% complete for SRR23279758_2.fastq.gz
Approx 95% complete for SRR23279758_2.fastq.gz
Started analysis of SRR23279758_1.fastq.gz
Approx 5% complete for SRR23279758_1.fastq.gz
Approx 10% complete for SRR23279758_1.fastq.gz
Approx 15% complete for SRR23279758_1.fastq.gz
Approx 20% complete for SRR23279758_1.fastq.gz
Approx 25% complete for SRR23279758_1.fastq.gz
Approx 30% complete for SRR23279758_1.fastq.gz
Approx 35% complete for SRR23279758_1.fastq.gz
Approx 40% complete for SRR23279758_1.fastq.gz
Approx 45% complete for SRR23279758_1.fastq.gz
Approx 50% complete for SRR23279758_1.fastq.gz
Approx 55% complete for SRR23279758_1.fastq.gz
Approx 60% complete for SRR23279758_1.fastq.gz
Approx 65% complete for SRR23279758_1.fastq.gz
Approx 70% complete for SRR23279758_1.fastq.gz
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Approx 80% complete for SRR23279758_1.fastq.gz
Approx 85% complete for SRR23279758_1.fastq.gz
Approx 90% complete for SRR23279758_1.fastq.gz
Approx 95% complete for SRR23279758_1.fastq.gz
Analysis complete for SRR23279758_2.fastq.gz
Analysis complete for SRR23279758_1.fastq.gz
^^^

         Please Stop The Program To Check The Error.         

^^^
---------------------------------------------------------------------------
commonError                               Traceback (most recent call last)
<ipython-input-7-8a7eaf688a48> in <module>
      7                 fragProfile=True,
      8                 report=True,
----> 9                 verbose=False)

/media/usb2/miniconda3/envs/cfDNApipe/lib/python3.6/site-packages/cfDNApipe/Pipeline.py in cfDNAWGBS(inputFolder, fastq1, fastq2, adapter1, adapter2, fastqcOP, idAdapter, idAdOP, rmAdapter, rmAdOP, bismarkOP, dudup, dudupOP, extractMethyOP, methyRegion, armCNV, CNV, fragProfile, deconvolution, report, verbose, box)
    415 
    416     # fastqc
--> 417     res_fastqc = fastqc(upstream=res_inputprocess, other_params=fastqcOP, verbose=verbose)
    418     results.update({"fastqc": res_fastqc})
    419 

/media/usb2/miniconda3/envs/cfDNApipe/lib/python3.6/site-packages/cfDNApipe/Fun_fastqc.py in __init__(self, fastqInput, fastqcOutputDir, threads, other_params, stepNum, upstream, verbose, **kwargs)
    102                 self.run(cmd)
    103             else:
--> 104                 self.multiRun(args=[cmd], func=None, nCore=1)
    105 
    106         self.stepInfoRec(cmds=[cmd], finishFlag=finishFlag)

/media/usb2/miniconda3/envs/cfDNApipe/lib/python3.6/site-packages/cfDNApipe/StepBase.py in multiRun(self, args, func, nCore)
    670             else:
    671                 print(mess)
--> 672                 raise commonError("Error occured in multi-core running!")
    673         else:  # check output for function
    674             output = [x[0] for x in results.get()]

commonError: Error occured in multi-core running!