BUG

[shangyf-stu]

Describe the bug A clear and concise description of what the bug is. zUMIs_YAMLerror.log only show 1

To Reproduce Provide the YAML file and full standard output. project: GSE117988 sequence_files: file1: name: /xtdisk/xiaojf_group/shangyf/a_result/Sequencing_data_quality_control/0_fastq/10x/GSE117988/SRR7722937/SRR7722937_S1_L001_I1_001.fastq.gz base_definition:

• BC(1-8) file2: name: /xtdisk/xiaojf_group/shangyf/a_result/Sequencing_data_quality_control/0_fastq/10x/GSE117988/SRR7722937/SRR7722937_S1_L001_R1_001.fastq.gz base_definition:
• BC(1-16)
• UMI(17-28) file3: name: /xtdisk/xiaojf_group/shangyf/a_result/Sequencing_data_quality_control/0_fastq/10x/GSE117988/SRR7722937/SRR7722937_S1_L001_R2_001.fastq.gz base_definition:
• cDNA(1-97) reference: STAR_index: /asnas/pmod/zengjy/softwares/STAR-master/bin/Linux_x86_64/index GTF_file: /asnas/pmod/zengjy/softwares/STAR-master/bin/Linux_x86_64/index additional_STAR_params: '--runMode alignReads --readFilesCommand zcat ' additional_files: ~ out_dir: /xtdisk/xiaojf_group/shangyf/a_result/Sequencing_data_quality_control/4_zUMIs/10x/GSE117988/SRR7722937 num_threads: 8 mem_limit: 0 filter_cutoffs: BC_filter: num_bases: 1 phred: 20 UMI_filter: num_bases: 1 phred: 20 barcodes: barcode_num: ~ barcode_file: '' barcode_sharing: shared_i7_bcs.txt automatic: yes BarcodeBinning: 0 nReadsperCell: 100 counting_opts: introns: yes downsampling: '0' strand: 0 Ham_Dist: 0 velocyto: no primaryHit: yes twoPass: yes make_stats: yes which_Stage: Filtering Rscript_exec: Rscript STAR_exec: STAR pigz_exec: pigz samtools_exec: samtools

Screenshots If applicable, add screenshots to help explain your problem.

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Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs

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Error: Syntax error loading yaml file Execution halted YAML file has an error. Look at the zUMIs_YAMLerror.log or contact developers.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Version [e.g. 22] CentOS 7.2.1511 samtools-1.9 r-3.6.1 pigz-2.4 star-2.7 Additional context Add any other context about the problem here. I want to process a 10x datasets, follow Protocol specific setup in wiki. I have checked checkyaml.R, what should I do? Anything would be appriciated!!

[cziegenhain]

Hi, Please share the error log text file here too! Most common issue would be a path that cannot be found. Note: You cannot give relative paths, please change barcode_sharing Also please remove your additional_STAR_params arguments, these basic things are taken care of by zUMIs.

Best, Christoph

[shangyf-stu]

the error log text file only show "1"

[LGCSherlock]

the error log text file only show "1"

Could you please tell me how you solved it?