taiji running problem #44
Description
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 GeneQuantHope your reply, THANK!