taiji running problem

[yuechaowu]

Hi kai,

When using Taiji, I encountered some issues while using a YAML file as input. The error message I encountered is:

there is my input.yml:

RNA-seq:
  - id: RNA_NIP_0h
    group: RNA_NIP_0h
    replicates:
      - rep: 1
        files:
          # Customized gene expression file
          - path: /home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_0h_rep1.txt
            tags: ['GeneQuant']
      - rep: 2
        files:
          # Customized gene expression file
          - path: /home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_0h_rep2.txt
            tags: ['GeneQuant']
      - rep: 3
        files:
          # Customized gene expression file
          - path: /home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_0h_rep3.txt
            tags: ['GeneQuant']

  - id: RNA_NIP_12h
    group: RNA_NIP_12h
    replicates:
      - rep: 1
        files:
          # Customized gene expression file
          - path: /home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_12h_rep1.txt
            tags: ['GeneQuant']
      - rep: 2
        files:
          # Customized gene expression file
          - path: /home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_12h_rep2.txt
            tags: ['GeneQuant']
      - rep: 3
        files:
          # Customized gene expression file
          - path: /home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_12h_rep3.txt
            tags: ['GeneQuant']

        

ATAC-seq:
  - id: ATAC_NIP_0h
    group: ATAC_NIP_0h
    replicates:
      - rep: 1
        files:
          - path: /home/wuyuechao/data3/project/rice_cold/bowtie2_mapping/ATAC_NIP_0h_rep1_unique_reDup.bam
            tags: ['Filtered', 'PairedEnd']
      - rep: 2
        files:
          - path: /home/wuyuechao/data3/project/rice_cold/bowtie2_mapping/ATAC_NIP_0h_rep2_unique_reDup.bam
            tags: ['Filtered', 'PairedEnd']

  - id: ATAC_NIP_12h
    group: ATAC_NIP_12h
    replicates:
      - rep: 1
        files:
          - path: /home/wuyuechao/data3/project/rice_cold/bowtie2_mapping/ATAC_NIP_12h_rep1_unique_reDup.bam
            tags: ['Filtered', 'PairedEnd']
      - rep: 2
        files:
          - path: /home/wuyuechao/data3/project/rice_cold/bowtie2_mapping/ATAC_NIP_12h_rep2_unique_reDup.bam
            tags: ['Filtered', 'PairedEnd']
       

When I switched from a YAML file to a TSV file, the previous error was resolved. However, I am still encountering some issues. I have set the "Filtered" tag in my BAM file, but when running Taiji, it still executes the "ATAC_Filter_Bam" step, which has been running for more than 4 hours without completion. I checked the background processes and found no CPU resources being utilized. Here is my TSV file:

type	id	group	rep	path	tags
ATAC-seq	ATAC_NIP_0h	ATAC_NIP_0h	1	/home/wuyuechao/data3/project/rice_cold/bowtie2_mapping/ATAC_NIP_0h_rep1_unique_reDup.bam	Filtered,PairedEnd
ATAC-seq	ATAC_NIP_0h	ATAC_NIP_0h	2	/home/wuyuechao/data3/project/rice_cold/bowtie2_mapping/ATAC_NIP_0h_rep2_unique_reDup.bam	Filtered,PairedEnd
ATAC-seq	ATAC_NIP_12h	ATAC_NIP_12h	1	/home/wuyuechao/data3/project/rice_cold/bowtie2_mapping/ATAC_NIP_12h_rep1_unique_reDup.bam	Filtered,PairedEnd
ATAC-seq	ATAC_NIP_12h	ATAC_NIP_12h	2	/home/wuyuechao/data3/project/rice_cold/bowtie2_mapping/ATAC_NIP_12h_rep2_unique_reDup.bam	Filtered,PairedEnd
RNA-seq	RNA_NIP_0h	RNA_NIP_0h	1	/home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_0h_rep1.txt	GeneQuant
RNA-seq	RNA_NIP_0h	RNA_NIP_0h	2	/home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_0h_rep2.txt	GeneQuant
RNA-seq	RNA_NIP_0h	RNA_NIP_0h	3	/home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_0h_rep3.txt	GeneQuant
RNA-seq	RNA_NIP_12h	RNA_NIP_12h	1	/home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_12h_rep1.txt	GeneQuant
RNA-seq	RNA_NIP_12h	RNA_NIP_12h	2	/home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_12h_rep2.txt	GeneQuant
RNA-seq	RNA_NIP_12h	RNA_NIP_12h	3	/home/wuyuechao/data3/project/rice_cold/plot_new/taiji/GeneQuant/RNA_NIP_12h_rep3.txt	GeneQuant

Hope your reply, THANK!

[yuechaowu]

The program ran into this error after running for a while.