<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>

CC BY-SA 4.0
2021-10-14T07:14:28.140Z
Do you see `bwa` under `/home/genetic/ncbi/dbGaP_26368/bwa_sam_CIRI`?
haci
CC BY-SA 4.0
2021-10-14T18:23:11.227Z
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?
Mohammad
CC BY-SA 4.0
2021-10-14T18:42:54.253Z
I believe adding `/bwa` right after `bwa` in your `tools:` section of the yaml file is worth a try.
haci
CC BY-SA 4.0
2021-10-17T09:30:55.880Z
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
Mohammad
CC BY-SA 4.0
2021-10-17T09:46:09.153Z
@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)
Mohammad
CC BY-SA 4.0
2021-10-17T18:21:19.470Z
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.
haci
<python>
Error in running CIRIquant package for 2 RNA-seq in Ubuntu 16.04
# Error in running CIRIquant package for 2 RNA-seq in Ubuntu 16.04

(Asked by: username_0 on 2021-10-14)

"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 
    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 @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?  
> **username_1**: I believe adding `/bwa` right after `bwa` in your `tools:` section of the yaml file is worth a try.  
> **username_0**: 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  
> **username_0**: @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)  
> **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.  

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## 0 answers

