Pair Extensions

[dozt...@gmail.com]

Hello everybody,

In the step1 of the HiC-Pro run I am getting this error:

'Nothing to align ! Please check input files and R1/R2 extension.'

My file scheme is like this:

+Input

++Sample1

+++f1_R1.fastq

+++f1_R2.fastq

and in my config-hicpro.txt Pair extensions are like this:

#########################################################################

## Data

#########################################################################

PAIR1_EXT = _R1

PAIR2_EXT = _R2

I am giving input folder as an input (-i) to HiC-Pro.

What am I doing wrong here?

Thanks for the replies. 

Regards.

[nservant]

Hi,
Everything looks good. Is it your real file name ?
Is it real fastq or fastq.gz extension ?
Could you give me your exact command line ?
Thank you

[dozt...@gmail.com]

Hi I forgot to add the details:
I am using SGE cluster and this error is showing up when I started the first run. I am getting the job files in output folder with the same command as in the Github documentation. After I got the first and second job files in the output folder I go into that folder and do qsub firstjobfile.sh
Do I have to move those files to the previous folder and give job submission command?

Files are .fastq and the names are f1_R1.fastq and f2_R2.fastq

Regards,
Dogancan

[nservant]

Everything looks good ...
In the output folder when you do you "qsub", you should have a file named "inputXXX"
Could you check that this file is not empty ?
One more question, which system are you using ?
And did it work in normal mode, without the -p option ?
Thanks

[dozt...@gmail.com]

Hi again,

There was a problem in input.txt file in the output folder. In the input.txt file the directory was written only for Pair extension 1. Also it was missing one folder. It was like this:

Sample1/f1_R1.fastq

I changed it to:

rawdata/Sample1/f1_R1.fastq

rawdata/Sample1/f1_R2.fastq

and it worked!

Regards,

Dogancan

1 Mart 2017 Çarşamba 11:39:38 UTC+2 tarihinde nservant yazdı:

[nservant]

This is normal. We also put the R1 file. The R2 file is detected by making a substitution of the two patterns you put in the configuration file.
So, it's strange. Adding the R2 should not fix your issue ...

[nservant]

Sorry, I was not clear enough in my answer. You should only have the R1 in the input file !

[nservant]

and you shoudn't have the "rawdata" in the path.
In theory, the path of your files is set using the RAW_DIR variable from your config file.
RAW_DIR = rawdata

Could you give me the exact command line you used to run HiCPro ?
In the output folder, you may have a rawdata link that point to your initial folder. Is it the case ?
Thanks

[dozt...@gmail.com]

Hi, 

- That's strange indeed. Here is my command in generating job files:

/mnt/kufs/scratch/dozturan15/HiC-Pro_2.8.0/bin/HiC-Pro -i sample1 -o sample1_output -c config-hicpro.txt -p

- I also tried with using Full PATH like I did for HiC-Pro command. Same results. 

- I have rawdata folder link that points to your initial folder, yes. 

- BTW, without using -p flag it is working without doing any extra work.

1 Mart 2017 Çarşamba 13:05:05 UTC+2 tarihinde nservant yazdı:

[dozt...@gmail.com]

I also tried with just R1 with adding rawdata in the beggining. It is also working. 

1 Mart 2017 Çarşamba 13:25:23 UTC+2 tarihinde dozt...@gmail.com yazdı:

[nservant]

If your inputs files are organized this way, you should put -i "Input" (and not "Sample1"). Is it what you did ?

+Input

++Sample1

+++f1_R1.fastq

+++f1_R2.fastq

[dozt...@gmail.com]

Yes that is exactly what I did. 

I have another question though. In the step1 job file is "-t 1-1" flag is necessary?

Dogancan

1 Mart 2017 Çarşamba 15:13:53 UTC+2 tarihinde nservant yazdı:

[nservant]

This flag is used if you want to process multiple samples in parallel
Let's say you have

+Input

++Sample1

+++f1_R1.fastq

+++f1_R2.fastq

+++f2_R1.fastq

+++f2_R2.fastq

++Sample1

+++f3_R1.fastq

+++f3_R2.fastq

All fastq pairs will be processed in parallel until the list of valid 3C products. So using -t1-3 here.

[dozt...@gmail.com]

Got it. But I deleted this line when I have just one sample and it gave me the very first error:

'Nothing to align ! Please check input files and R1/R2 extension.'

1 Mart 2017 Çarşamba 17:12:20 UTC+2 tarihinde nservant yazdı:

[dozt...@gmail.com]

So as a result: 

1. When I deleted the -t flag in the job file it is giving me "Nothing to align! Check the extensions R1/R2" error.

2. When I keep the -t flag it gives me python error in saying that it is not found. Although the path is correct:

I did not resolve the first problem. But my second problem was originated from python path itself. So it is solved. 

2 Mart 2017 Perşembe 12:27:26 UTC+2 tarihinde dozt...@gmail.com yazdı:

[Wen Zhang]

Hi Dogancan,

I also met this issue right now. Did you solve it?

Could you please let me know what the problem that is?

Thank you,

Wen