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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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Error. Failed: Could not find transcript_id #30

Closed jrose835 closed 2 years ago

jrose835 commented 2 years ago

Hello,

I am having trouble running taiji (v1.2.1.3) on some human RNAseq/ATACseq data which ends with this error:

[ERROR][07-29 18:51] ^[[0m^[[0m^[[31mRNA_Convert_ID_To_Name(deb6..) Failed: could not find "transcript_id"
CallStack (from HasCallStack):
  error, called at src/Bio/RealWorld/GENCODE.hs:96:26 in bioinformatics-toolkit-0.9.5-3mVlLPWw5KFJ8YTMh3VDIA:Bio.RealWorld.GENCODE
CallStack (from HasCallStack):
  error, called at src/Control/Workflow/Interpreter/Exec.hs:143:37 in SciFlow-0.7.2-TntpNqG8TaLOeICwjTwEt:Control.Workflow.Interpreter.Exec

After double-checking my input and config files (pasted below), I still can't seem to figure out what is causing this error. Any advice would be very helpful.

Thank you!

Code run: taiji run --config config.yml

Input.yml

ATAC-Seq:
  - id: SLE_rN_highDA_ATAC
    group: SLE_rN_highDA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.1929.1537.rN/SLE.1929.1537.rN.MACS2.Peaks/SLE.1929.1537.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 2
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.1551.1597.rN/SLE.1551.1597.rN.MACS2.Peaks/SLE.1551.1597.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 3
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.1731.1738.rN/SLE.1731.1738.rN.MACS2.Peaks/SLE.1731.1738.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 4
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2711.871.rN/SLE.2711.871.rN.MACS2.Peaks/SLE.2711.871.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 5
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.3202.2491.rN/SLE.3202.2491.rN.MACS2.Peaks/SLE.3202.2491.rN_peaks.narrowPeak
            format: NarrowPeak

  - id: SLE_T1T2_highDA_ATAC
    group: SLE_T1T2_highDA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.1929.1537.T1-2/SLE.1929.1537.T1-2.MACS2.Peaks/SLE.1929.1537.T1-2_peaks.narrowPeak
            format: NarrowPeak

  - id: HC_rN_NA_ATAC
    group: HC_rN_NA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/HCD.918.1215.rN/HCD.918.1215.rN.MACS2.Peaks/HCD.918.1215.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 2
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/HCD.646.1234.rN/HCD.646.1234.rN.MACS2.Peaks/HCD.646.1234.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 3
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/HCD.796.1235.rN/HCD.796.1235.rN.MACS2.Peaks/HCD.796.1235.rN_peaks.narrowPeak
            format: NarrowPeak
     - rep: 4
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/HCD.1171.1296.rN/HCD.1171.1296.rN.MACS2.Peaks/HCD.1171.1296.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 5
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/HCD.878.1606.rN/HCD.878.1606.rN.MACS2.Peaks/HCD.878.1606.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 6
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/HCD.875.1610.rN/HCD.875.1610.rN.MACS2.Peaks/HCD.875.1610.rN_peaks.narrowPeak
            format: NarrowPeak

  - id: HC_T1T2_NA_ATAC
    group: HC_T1T2_NA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/HCD.918.1215.T1-2/HCD.918.1215.T1-2.MACS2.Peaks/HCD.918.1215.T1-2_peaks.narrowPeak
            format: NarrowPeak
      - rep: 2
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/HCD.646.1234.T1-2/HCD.646.1234.T1-2.MACS2.Peaks/HCD.646.1234.T1-2_peaks.narrowPeak
            format: NarrowPeak
      - rep: 3
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/HCD.1171.1296.T1-2/HCD.1171.1296.T1-2.MACS2.Peaks/HCD.1171.1296.T1-2_peaks.narrowPeak
            format: NarrowPeak
      - rep: 4
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/HCD.875.1610.T1-2/HCD.875.1610.T1-2.MACS2.Peaks/HCD.875.1610.T1-2_peaks.narrowPeak
            format: NarrowPeak

  - id: SLE_rN_lowDA_ATAC
    group: SLE_rN_lowDA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2913.559.rN/SLE.2913.559.rN.MACS2.Peaks/SLE.2913.559.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 2
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2911.2209.rN/SLE.2911.2209.rN.MACS2.Peaks/SLE.2911.2209.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 3
       files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2932.3240.rN/SLE.2932.3240.rN.MACS2.Peaks/SLE.2932.3240.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 4
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.3136.3378.rN/SLE.3136.3378.rN.MACS2.Peaks/SLE.3136.3378.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 5
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2891.420.rN/SLE.2891.420.rN.MACS2.Peaks/SLE.2891.420.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 6
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2880.3039.rN/SLE.2880.3039.rN.MACS2.Peaks/SLE.2880.3039.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 7
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2900.3328.rN/SLE.2900.3328.rN.MACS2.Peaks/SLE.2900.3328.rN_peaks.narrowPeak
            format: NarrowPeak
      - rep: 8
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2898.3314.rN/SLE.2898.3314.rN.MACS2.Peaks/SLE.2898.3314.rN_peaks.narrowPeak
            format: NarrowPeak

  - id: SLE_T1T2_lowDA_ATAC
    group: SLE_T1T2_lowDA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2913.559.T1-2/SLE.2913.559.T1-2.MACS2.Peaks/SLE.2913.559.T1-2_peaks.narrowPeak
            format: NarrowPeak
      - rep: 2
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2911.2209.T1-2/SLE.2911.2209.T1-2.MACS2.Peaks/SLE.2911.2209.T1-2_peaks.narrowPeak
            format: NarrowPeak
      - rep: 3
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2891.420.T1-2/SLE.2891.420.T1-2.MACS2.Peaks/SLE.2891.420.T1-2_peaks.narrowPeak
            format: NarrowPeak
      - rep: 4
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/data/SLE.2900.3328.T1-2/SLE.2900.3328.T1-2.MACS2.Peaks/SLE.2900.3328.T1-2_peaks.narrowPeak
            format: NarrowPeak

RNA-Seq:
  - id: SLE_rN_highDA_RNA
    group: SLE_rN_highDA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.0.3621.rN/SLE.0.3621.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.0.1537.rN/SLE.0.1537.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.0.1597.rN/SLE.0.1597.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 4
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.0.1738.rN/SLE.0.1738.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 5
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2711.871.rN/SLE.2711.871.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 6
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.3202.2491.rN/SLE.3202.2491.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 7
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.3039.3553.rN/SLE.3039.3553.rN.rpkm.tsv
            tags: ['GeneQuant']

  - id: SLE_T1T2_highDA_RNA
    group: SLE_T1T2_highDA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.0.3651.T1T2/SLE.0.3651.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.0.1537.T1T2/SLE.0.1537.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.0.1597.T1T2/SLE.0.1597.T1T2.rpkm.tsv
            tags: ['GeneQuant']
    - rep: 4
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.0.1738.T1T2/SLE.0.1738.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 5
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2711.871.T1T2/SLE.2711.871.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 6
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.3202.2491.T1T2/SLE.3202.2491.T1T2.rpkm.tsv
            tags: ['GeneQuant']

  - id: HC_rN_NA_RNA
    group: HC_rN_NA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/HCD.918.1215.rN/HCD.918.1215.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/HCD.646.1234.rN/HCD.646.1234.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/HCD.796.1235.rN/HCD.796.1235.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 4
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/HCD.1171.1296.rN/HCD.1171.1296.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 5
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/HCD.878.1606.rN/HCD.878.1606.rN.rpkm.tsv
            tags: ['GeneQuant']

  - id: HC_T1T2_NA_RNA
    group: HC_T1T2_NA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/HCD.918.1215.T1T2/HCD.918.1215.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/HCD.646.1234.T1T2/HCD.646.1234.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/HCD.796.1235.T1T2/HCD.796.1235.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 4
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/HCD.1171.1296.T1T2/HCD.1171.1296.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 5
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/HCD.878.1606.T1T2/HCD.878.1606.T1T2.rpkm.tsv
            tags: ['GeneQuant']

  - id: SLE_rN_lowDA_RNA
    group: SLE_rN_lowDA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2913.559.rN/SLE.2913.559.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2911.2209.rN/SLE.2911.2209.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2932.3240.rN/SLE.2932.3240.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 4
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.3136.3378.rN/SLE.3136.3378.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 5
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2891.420.rN/SLE.2891.420.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 6
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2880.3039.rN/SLE.2880.3039.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 7
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2900.3328.rN/SLE.2900.3328.rN.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 8
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2898.3314.rN/SLE.2898.3314.rN.rpkm.tsv
            tags: ['GeneQuant']
     - rep: 9
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2893.428.rN/SLE.2893.428.rN.rpkm.tsv
            tags: ['GeneQuant']

  - id: SLE_T1T2_lowDA_RNA
    group: SLE_T1T2_lowDA
    replicates:
      - rep: 1
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2913.559.T1T2/SLE.2913.559.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2911.2209.T1T2/SLE.2911.2209.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2932.3240.T1T2/SLE.2932.3240.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 4
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.3136.3378.T1T2/SLE.3136.3378.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 5
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2891.420.T1T2/SLE.2891.420.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 6
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2880.3039.T1T2/SLE.2880.3039.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 7
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2900.3328.T1T2/SLE.2900.3328.T1T2.rpkm.tsv
            tags: ['GeneQuant']
      - rep: 8
        files:
          - path: /home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_RNA/data2/SLE.2898.3314.T1T2/SLE.2898.3314.T1T2.rpkm.tsv
            tags: ['GeneQuant']

config.yml

################################################################################
# The meaning of each field is explained at:
# https://taiji-pipeline.github.io/documentation/options.html
################################################################################

################################################################################
# Minimal settings
################################################################################

input: "input.yml"

output_dir: "/home/boss_lab/Projects/ACE_Collaborations/AutoimmuneDisease_rN_T12/ACE_rN_T12_ATAC/ATAC_concat/analysis/PageRank/run2_JR/output/"

# Replace, this will download the genome into the output directory
# Options: mm10, hg38, GRCh38, GRCm38
#assembly: "mm10" # Replace, this will download the genome into the output directory

################################################################################
# Advanced settings
################################################################################

# Replace, options: HG38.nohap.fa hg38.eGFP.fa lambda.J02459.1.fa mm10.fa mm10_ERCC.fa rn6.ERCC.fa phiX174.fa 
genome: "/home/boss_lab/Apps/genomes/fasta/HG38.nohap.fa"

# Replace, options: hg38_gencodeV27.gtf mm10.gencode.vM17.gtf rn6.refGene.gtf
annotation: "/home/boss_lab/Apps/genomes/fasta/hg38_gencodeV27.gtf"

# Replace, options: cisBP_mouse.meme, cisBP_human.meme
motif_file: "/home/boss_lab/Apps/bitbucket/pagerank/taiji-1.2.1.3-formatting/cisBP_human.meme"

# TODO
#genome_index: ""

# Replace, options: HG38.nohap hg38.eGFP mm10.ERCC rn6.ERCC
bwa_index: "/home/boss_lab/Apps/genomes/bwa/HG38.nohap"

# Replace, options: hg38.ERCC.STAR-2.7.0f hg38.nohap hg38.nohap.ERCC.eGFP index_scripts mm10.ERCC rn6.ERCC
#star_index: "/home/boss_lab/Apps/genomes/STAR/hg38.nohap"

#rsem_index: ""

#callpeak_fdr: 0.01

#callpeak_genome_size: "" # options: hs

#tss_enrichment_cutoff: 5

System info: Taiji-v1.2.1.3 Linux Distributor ID: Ubuntu Description: Ubuntu 20.04.4 LTS Release: 20.04 Codename: focal

kaizhang commented 2 years ago

There may be some problems in your gene annotation file.

annotation: "/home/boss_lab/Apps/genomes/fasta/hg38_gencodeV27.gtf"

Can you share this file with me?

jrose835 commented 2 years ago

Thanks so much for getting back to me so quick. The file is a little large but here is the head:


##description: evidence-based annotation of the human genome (GRCh38), version 27 (Ensembl 90)
##provider: GENCODE
##contact: gencode-help@sanger.ac.uk
##format: gtf
##date: 2017-08-01
chr1    HAVANA  gene    11869   14409   .   +   .   gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1    HAVANA  transcript  11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    11869   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    12613   12721   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    13221   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
kaizhang commented 2 years ago

The head looks fine to me. I would like to get the complete file to see if I can reproduce the error. Would you be able to compress it and share that with me using Google Drive or Dropbox?

jrose835 commented 2 years ago

Turns out using a newer version of annotation allows the program to complete successfully. I've sent you the old annotation file if you'd like to check it out. Let me know if you don't see it. Thanks for your help!