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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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Exception: The chemistry and darkreaction are unable to be automatically determined. #76

Closed Xxhongs closed 4 weeks ago

Xxhongs commented 4 weeks ago

您好，在进行Chemistry(darkreaction) determined in oligoR2 : darkreaction步骤时，出现以下错误，我注意到帮助文档中提示了“If automatic identification fails or is incorrect, manual settings can be applied using --chemistry and --darkreaction. The --chemistry option includes "scRNAv1HT", "scRNAv2HT", and "scRNAv3HT", while the --darkreaction option uses commas to separate cDNA and oligo settings, such as "R1,R1R2", "R1,R1", "unset,unset", etc., where "R1,R1R2" indicates a dark reaction set for cDNA R1 and oligo R1R2”。您能具体解释一下该如何确定具体的--darkreaction option和--chemistry option吗？ 值得注意的是，使用同样代码处理同批的其他数据能正常运行。

Chemistry(darkreaction) determined in oligoR1 : darkreaction Chemistry(darkreaction) determined in oligoR2 : darkreaction Valid chemistry read counts percent < 0.5 Traceback (most recent call last): File "/public//soft/Miniconda/envs/DNBC4toolsV2/bin/dnbc4tools", line 8, in sys.exit(main()) File "/public//soft/Miniconda/envs/DNBC4toolsV2/lib/python3.8/site-packages/dnbc4tools/dnbc4tools.py", line 110, in main args.func(args) File "/public//soft/Miniconda/envs/DNBC4toolsV2/lib/python3.8/site-packages/dnbc4tools/rna/data.py", line 169, in data Data(args).run() File "/public//soft/Miniconda/envs/DNBC4toolsV2/lib/python3.8/site-packages/dnbc4tools/rna/data.py", line 87, in run cDNAconfig, oligoconfig = self.seqStructure() File "/public//soft/Miniconda/envs/DNBC4toolsV2/lib/python3.8/site-packages/dnbc4tools/rna/data.py", line 55, in seqStructure cDNAconfig = designated_chem_dark( File "chemistydark.py", line 371, in dnbc4tools.tools.chemistydark.designated_chem_dark File "chemistydark.py", line 265, in dnbc4tools.tools.chemistydark.check_fastqlist File "chemistydark.py", line 102, in dnbc4tools.tools.chemistydark.check_fastq_chemistry Exception: The chemistry and darkreaction are unable to be automatically determined.

Traceback (most recent call last): File "/public//soft/Miniconda/envs/DNBC4toolsV2/bin/dnbc4tools", line 8, in sys.exit(main()) File "/public//soft/Miniconda/envs/DNBC4toolsV2/lib/python3.8/site-packages/dnbc4tools/dnbc4tools.py", line 110, in main args.func(args) File "/public//soft/Miniconda/envs/DNBC4toolsV2/lib/python3.8/site-packages/dnbc4tools/rna/run.py", line 144, in run Runpipe(args).runpipe() File "/public//soft/Miniconda/envs/DNBC4toolsV2/lib/python3.8/site-packages/dnbc4tools/rna/run.py", line 131, in runpipe start_print_cmd(pipecmd,os.path.join(self.outdir,self.name)) File "/public//soft/Miniconda/envs/DNBC4toolsV2/lib/python3.8/site-packages/dnbc4tools/tools/utils.py", line 138, in start_print_cmd subprocess.check_call(arg, shell=True) File "/public//soft/Miniconda/envs/DNBC4toolsV2/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/public//soft/Miniconda/envs/DNBC4toolsV2/bin/dnbc4tools rna data --cDNAfastq1 cDNA/E150019379_L01_79_1.fq.gz,cDNA/E150019379_L01_87_1.fq.gz,cDNA/E150019379_L01_95_1.fq.gz,cDNA/E150019379_L01_79_2.fq.gz,cDNA/E150019379_L01_87_2.fq.gz,cDNA/E150019379_L01_95_2.fq.gz --cDNAfastq2 cDNA/E150019379_L01_79_1.fq.gz,cDNA/E150019379_L01_87_1.fq.gz,cDNA/E150019379_L01_95_1.fq.gz,cDNA/E150019379_L01_79_2.fq.gz,cDNA/E150019379_L01_87_2.fq.gz,cDNA/E150019379_L01_95_2.fq.gz --oligofastq1 oligo/558_oligo_1.fq.gz --oligofastq2 oligo/558_oligo_2.fq.gz --threads 10 --name 558 --chemistry auto --darkreaction auto --outdir /public2/data/wangjunhao/data/MGI_SingCell/HT_scRNA-analysis/Vesion2/result --genomeDir /public//reference/hg38/MGI/DNBelab_C_Series_HT_scRNA/GRCh38V2 --gtf /public//reference/hg38/MGI/DNBelab_C_Series_HT_scRNA/GRCh38V2/genes.filter.gtf --chrMT chrM' returned non-zero exit status 1.

lishuangshuang0616 commented 4 weeks ago 
--cDNAfastq1 cDNA/E150019379_L01_79_1.fq.gz,cDNA/E150019379_L01_87_1.fq.gz,cDNA/E150019379_L01_95_1.fq.gz,cDNA/E150019379_L01_79_2.fq.gz,cDNA/E150019379_L01_87_2.fq.gz,cDNA/E150019379_L01_95_2.fq.gz
--cDNAfastq2 cDNA/E150019379_L01_79_1.fq.gz,cDNA/E150019379_L01_87_1.fq.gz,cDNA/E150019379_L01_95_1.fq.gz,cDNA/E150019379_L01_79_2.fq.gz,cDNA/E150019379_L01_87_2.fq.gz,cDNA/E150019379_L01_95_2.fq.gz

Are the fastqs not correctly? Correct like this.

--cDNAfastq1 cDNA/E150019379_L01_79_1.fq.gz,cDNA/E150019379_L01_87_1.fq.gz,cDNA/E150019379_L01_95_1.fq.gz
--cDNAfastq2 cDNA/E150019379_L01_79_2.fq.gz,cDNA/E150019379_L01_87_2.fq.gz,cDNA/E150019379_L01_95_2.fq.gz
Xxhongs commented 4 weeks ago

原来是这么简单的错误，非常感谢！