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Taiji-pipeline / Taiji

All-in-one analysis pipeline
https://taiji-pipeline.github.io/
BSD 3-Clause "New" or "Revised" License
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taiji running problem #44

Open yuechaowu opened 5 months ago

yuechaowu commented 5 months ago

Hi kai,

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

Xnip2024-01-12_16-56-54

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 commented 5 months ago

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

image