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"CIRIquant" is a Python package for detecting Circular RNA. I ran "CIRIquant" individually and it was run. consequently, I ran CIRIquant through the below command and parameters in the terminal:

 ~/.local/bin/CIRIquant -t  4

     -1 ./SRR1176949_1.fastq.gz     
     -2 ./SRR1176949_2.fastq.gz 
     --config ./CIRIquant-Config.yml              
     -o ./SRR1176949   
     -p  SRR1176949

But I got the below message:

Traceback (most recent call last):
  File "/home/genetic/.local/bin/CIRIquant", line 11, in <module>
    sys.exit(main())
  File "/home/genetic/.local/lib/python2.7/site-packages/CIRIquant/main.py", line 89, in main
    config = check_config(check_file(args.config_file))
  File "/home/genetic/.local/lib/python2.7/site-packages/CIRIquant/utils.py", line 82, in check_config
    globals()[i.upper()] = check_file(config['tools'][i])
  File "/home/genetic/.local/lib/python2.7/site-packages/CIRIquant/utils.py", line 49, in check_file
    raise ConfigError('File: {}, not found'.format(file_name))
CIRIquant.utils.ConfigError: File: /home/genetic/ncbi/dbGaP_26368/bwa_sam_CIRI/bwa, not found

########### My "CIRIquant-Config.yml" content is as below:

tools:
  bwa: /home/genetic/ncbi/dbGaP_26368/bwa_sam_CIRI/bwa
  hisat2: /usr/bin/hisat2-2.2.1
  stringtie: /usr/bin/stringtie
  samtools: /usr/bin/samtools-1.9

reference:
  fasta: /home/genetic/ncbi/dbGaP-26368/fasta_file/hg19.fa
  gtf: /home/genetic/ncbi/dbGaP-26368/gtf_file/gencode.v19.annotation.gtf
  bwa_index: /home/genetic/ncbi/dbGaP-26368/bwa-sam-CIRI/bwa-0.7.17/hg19
  hisat_index: /usr/bin/hisat2-2.2.1/hg19

I apprecite it if anyone share his/her comments with me.

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    $\begingroup$ Do you see bwa under /home/genetic/ncbi/dbGaP_26368/bwa_sam_CIRI? $\endgroup$
    – haci
    Oct 14 at 7:14
  • $\begingroup$ Dear @haci , I installed bwa aligner in bwa folder. In fact, in "/home/genetic/ncbi/dbGaP_26368/bwa_sam_CIRI/bwa" bwa is a folder and the executive file of bwa is in bwa folder. should I Change this path structure? $\endgroup$
    – Mohammad
    Oct 14 at 18:23
  • 1
    $\begingroup$ I believe adding /bwa right after bwa in your tools: section of the yaml file is worth a try. $\endgroup$
    – haci
    Oct 14 at 18:42
  • $\begingroup$ Dear @haci, I did your recommendation in tools : section and was passed but Now I have the same error for refrence : section for fasta file as below: CIRIquant.utils.ConfigError: File:/home/genetic/ncbi/dbGaP-26368/fasta_file/hg19.fa , not found . I appreciate it if you share your comments with me $\endgroup$
    – Mohammad
    Oct 17 at 9:30
  • 1
    $\begingroup$ Once again, do you see hg19.fa under /home/genetic/ncbi/dbGaP-26368/fasta_file/? h19.fa.gz is not the same as hg19.fa, the former is compressed. Most aligners if not all are capable of working on compressed fasta files so you can give a try by altering reference section in your yaml file to reflect that. $\endgroup$
    – haci
    Oct 17 at 18:21

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