MakeBigWig Issue

[phoebe460]

Hi Kai,

So I've decided to make a new input file, but now starting from my .BAM files with the tag 'PairedEnd' and same RNA quantification files like before. I've been running into the following error when trying to make BigWig files:

Do you know how to resolve this? I've placed the libssl.so.1.0.0 in my $PATH directory -> /.local/bin and I am still getting the same error. Any insights regarding this? Any help would be much appreciated again! Thank you!

[phoebe460]

As followup from discussion on Slack:

Here is my input file after making the changes.

RNA-seq:
  - group: 'NDC'
    id: 'NDC_RNA'
    replicates:
      - rep: 1
        files:
          #Customized gene expression file
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_NDC-1.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          #Customized gene expression file
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_NDC-2.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          #Customized gene expression file
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_NDC-3.tsv
            tags: ['GeneQuant']
  - group: 'V717I'
    id: 'V717I_RNA'
    replicates:
      - rep: 1
        files:
          #Customized gene expression file
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_V717I-1.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          #Customized gene expression file
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_V717I-2.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          #Customized gene expression file                                                     
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_V717I-3.tsv                            
            tags: ['GeneQuant']
  - group: 'A79V'
    id: 'A79V_RNA'
    replicates:
      - rep: 1
        files:
          #Customized gene expression file
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_A79V-1.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          #Customized gene expression file
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_A79V-2.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          #Customized gene expression file                                                     
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_A79V-3.tsv                            
            tags: ['GeneQuant']
  - group: 'N141I'
    id: 'N141I_RNA'
    replicates:
      - rep: 1
        files:
          #Customized gene expression file
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_N141I-1.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          #Customized gene expression file
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_N141I-2.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          #Customized gene expression file                                                     
          - path: /home/prvaldes/scratch/Taiji/RNA-seq-counts/RNA-seq-counts_Taiji_N141I-3.tsv                            
            tags: ['GeneQuant']

ATAC-seq:
  - group: 'NDC'
    id: 'NDC_ATAC'
    replicates:
      - rep: 1
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/NDC_1.bam
          tags: ['PairedEnd', 'Filtered']
      - rep: 2
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/NDC_2.bam
          tags: ['PairedEnd', 'Filtered']
      - rep: 3
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/NDC_3.bam
          tags: ['PairedEnd', 'Filtered']
  - group: 'V717I'
    id: 'V717I_ATAC'
    replicates:
      - rep: 1
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/V717I_1.bam
          tags: ['PairedEnd', 'Filtered']
      - rep: 2
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/V717I_2.bam
          tags: ['PairedEnd', 'Filtered']  
      - rep: 3
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/V717I_3.bam
          tags: ['PairedEnd', 'Filtered'] 
  - group: 'A79V'
    id: 'A79V_ATAC'
    replicates:
      - rep: 1
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/A79V_1.bam
          tags: ['PairedEnd', 'Filtered']
      - rep: 2
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/A79V_2.bam
          tags: ['PairedEnd', 'Filtered']  
      - rep: 3
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/A79V_3.bam
          tags: ['PairedEnd', 'Filtered'] 
  - group: 'N141I'
    id: 'N141I_ATAC'
    replicates:
      - rep: 1
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/N141I_1.bam
          tags: ['PairedEnd', 'Filtered']
      - rep: 2
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/N141I_2.bam
          tags: ['PairedEnd', 'Filtered']
      - rep: 3
        files: 
        - path: /home/prvaldes/scratch/diffTF/input/data/bam/N141I_3.bam
          tags: ['PairedEnd', 'Filtered'] 

So far, no errors when running with the new input file, so will keep you updated if I run into other issues. Thanks again!

[kaizhang]

Please make sure your bedGraphToBigWig installation is working. It looks like you have installed it at this location:

 /home/prvaldes/anaconda3/bin/bedGraphToBigWig

Just type /home/prvaldes/anaconda3/bin/bedGraphToBigWig to see if there is any problem.

At the very least, you can get all results except bigwig files even with this problem.

[phoebe460]

So I think I am able to run the bedGraphToBigWig command now, but now I get a new error:

It says CHR not found: chr12. I've been using the GRCh38 assembly intially provided with the tool, so not sure what is going on here. Any suggestions?