Error in rule gap_realign about pseudou-bidseq

[y9c]

Hi @Jarvis559,

Could you attach the full log file for debugging?

[Jarvis559]

2024-01-10T125527.473221.snakemake.log

[y9c]

Seem that the log file is incomplete, which does not show the command that was used. What is the reference sequence you used in the data.yaml file.

[Jarvis559]

Thanks for your reply! This is my first test data.yaml file:

reference:
  contamination:
    fa: /disk/user_18/jky_project/genome/Mesomycoplasma_hyorhinis_ATCC_17981/Mesomycoplasma_hyorhinis_ATCC_17981.fna
  genes:
    fa: /disk/user_18/jky_project/genome/GRCh38.p14/GRCh38.p14.sncRNA.fa
  genome:
    fa: /disk/user_18/jky_project/genome/GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.fna
    star: /disk/user_18/jky_project/index/star/GRCh38.p14/GRCh38.p14

samples:
  HeLaWT-rep1-input:
    data:
      - R1: /disk/user_18/jky_project/BID_project/learning/rawdata/HeLa_input_1.fastq.gz
    group: HeLaWT
    treated: false
  HeLaWT-rep1-treated:
    data:
      - R1: /disk/user_18/jky_project/BID_project/learning/rawdata/HeLa_BID_1.fastq.gz
    group: HeLaWT
    treated: true
  HeLaWT-rep2-treated:
    data:
      - R1: /disk/user_18/jky_project/BID_project/learning/rawdata/HeLa_BID_2.fastq.gz
    group: HeLaWT
    treated: true

And now i am trying the second test without the input of contamination reference genome sequence:

# Max number of cores for all the running jobs at the same time
cores: 50

barcode: "NNNNNXXX-XXXNNNNNATCACG"


# NOTE: relative path of reference and sample data should relative to current config file, rather than workdir
reference:
  genes:
    fa: /disk/user_18/jky_project/genome/GRCh38.p14/GRCh38.p14.sncRNA.fa
  genome:
    fa: /disk/user_18/jky_project/genome/GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.fna
    star: /disk/user_18/jky_project/index/star/GRCh38.p14/GRCh38.p14

samples:
  HeLaWT-rep1-input:
    data:
      - R1: /disk/user_18/jky_project/BID_project/learning/rawdata/HeLa_input_1.fastq.gz
    group: HeLaWT
    treated: false
  HeLaWT-rep1-treated:
    data:
      - R1: /disk/user_18/jky_project/BID_project/learning/rawdata/HeLa_BID_1.fastq.gz
    group: HeLaWT
    treated: true
  HeLaWT-rep2-treated:
    data:
      - R1: /disk/user_18/jky_project/BID_project/learning/rawdata/HeLa_BID_2.fastq.gz
    group: HeLaWT
    treated: true

[y9c]

This likely that the data you used did not contain reads that mapped to the "Mesomycoplasma_hyorhinis_ATCC_17981" reference which lead to zero size of bam file.

[Jarvis559]

I will see if removing the step of alignment to the Mesomycoplasma_hyorhinis_ATCC_17981 genome works. Thank you very much!

[Jarvis559]

Hi y9c!

Removing the step of alignment to the Mesomycoplasma_hyorhinis_ATCC_17981 genome works!

But I encountered two instances of automatic program termination. My command is nohup apptainer run docker://y9ch/bidseq & in the terminal. And I always keep the terminal on. The attatchment is the two log files.
2024-01-11T111942.665433.snakemake.log
2024-01-12T003946.169422.snakemake.log

[y9c]

Great! If there are more questions, please let me know.