Body: <p>&quot;<a href="https://ciri-cookbook.readthedocs.io/en/latest/CIRIquant_2_quantification.html" rel="nofollow noreferrer">CIRIquant</a>&quot; is a Python package for detecting Circular RNA. I ran &quot;CIRIquant&quot; individually and it was run. consequently, I ran CIRIquant through the below command and parameters in the terminal:</p>
  <pre><code> ~/.local/bin/CIRIquant -t  4
  
       -1 ./SRR1176949_1.fastq.gz     
       -2 ./SRR1176949_2.fastq.gz 
       --config ./CIRIquant-Config.yml              
       -o ./SRR1176949   
       -p  SRR1176949
  </code></pre>
  <p>But I got the below message:</p>
  <pre><code>Traceback (most recent call last):
    File &quot;/home/genetic/.local/bin/CIRIquant&quot;, line 11, in &lt;module&gt;
      sys.exit(main())
    File &quot;/home/genetic/.local/lib/python2.7/site-packages/CIRIquant/main.py&quot;, line 89, in main
      config = check_config(check_file(args.config_file))
    File &quot;/home/genetic/.local/lib/python2.7/site-packages/CIRIquant/utils.py&quot;, line 82, in check_config
      globals()[i.upper()] = check_file(config['tools'][i])
    File &quot;/home/genetic/.local/lib/python2.7/site-packages/CIRIquant/utils.py&quot;, 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
  </code></pre>
  <p>###########
  My &quot;CIRIquant-Config.yml&quot; content is as below:</p>
  <pre><code>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
  </code></pre>
  <p>I apprecite it if anyone share his/her comments with me.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-14T07:14:28.140Z
Comments.Text: Do you see `bwa` under `/home/genetic/ncbi/dbGaP_26368/bwa_sam_CIRI`?
Comments.UserDisplayName: haci
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-14T18:23:11.227Z
Comments.Text: 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?
Comments.UserDisplayName: Mohammad
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-14T18:42:54.253Z
Comments.Text: I believe adding `/bwa` right after `bwa` in your `tools:` section of the yaml file is worth a try.
Comments.UserDisplayName: haci
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-17T09:30:55.880Z
Comments.Text: 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
Comments.UserDisplayName: Mohammad
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-17T09:46:09.153Z
Comments.Text: @haci I downloaded hg19.fa from : [link] (https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/)     through this link:   [link] (https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz)
Comments.UserDisplayName: Mohammad
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-17T18:21:19.470Z
Comments.Text: 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.
Comments.UserDisplayName: haci
Tags: <python>
Title: Error in running CIRIquant package for 2 RNA-seq in Ubuntu 16.04
ThreadText: # Error in running CIRIquant package for 2 RNA-seq in Ubuntu 16.04
  
  (Asked by: username_0 on 2021-10-14)
  
  "[CIRIquant](https://ciri-cookbook.readthedocs.io/en/latest/CIRIquant_2_quantification.html)" 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.
  
  **Tags:** python
  
  > **Comments:**
  > **username_1**: Do you see `bwa` under `/home/genetic/ncbi/dbGaP_26368/bwa_sam_CIRI`?  
  > **username_0**: Dear @username_1 , 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?  
  > **username_1**: I believe adding `/bwa` right after `bwa` in your `tools:` section of the yaml file is worth a try.  
  > **username_0**: Dear @username_1, 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  
  > **username_0**: @username_1 I downloaded hg19.fa from : [link] (https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/)     through this link:   [link] (https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz)  
  > **username_1**: 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.  
  
  ---
  
  ## 0 answers
  
  