Hi Jayaram,

You need to provide more detail for me to help you. What are you having difficulty with, and where exactly in the QIIME pipeline?

Let me know exactly what, and I will be able to assist a bit more.

The QIIME website has great tutorials and help pages.

Hope this helps.

Andries

http://nbviewer.jupyter.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb

http://qiime.org/

http://qiime.org/scripts/index.html

Hi Andries,

Thank you for the response.

I installed the base qiime

Initially I tried to merge the fastq fiiles. With the given script. I got the following error. Please have a look

Traceback (most recent call last):

File "/home/jayaram/miniconda2/envs/qiime1/bin/join_paired_ends.py", line 4, in

__import__('pkg_resources').run_script('qiime==1.9.1', 'join_paired_ends.py')

File "/home/jayaram/miniconda2/envs/qiime1/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 744, in run_script

File "/home/jayaram/miniconda2/envs/qiime1/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 1499, in run_script

File "/home/jayaram/miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/join_paired_ends.py", line 178, in

main()

File "/home/jayaram/miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/join_paired_ends.py", line 155, in main

working_dir=output_dir)

File "/home/jayaram/miniconda2/envs/qiime1/lib/python2.7/site-packages/burrito_fillings-0.1.1-py2.7.egg/bfillings/fastq_join.py", line 180, in join_paired_end_reads_fastqjoin

File "/home/jayaram/miniconda2/envs/qiime1/lib/python2.7/site-packages/burrito-0.9.1-py2.7.egg/burrito/util.py", line 201, in __init__

File "/home/jayaram/miniconda2/envs/qiime1/lib/python2.7/site-packages/burrito-0.9.1-py2.7.egg/burrito/util.py", line 468, in _error_on_missing_application

burrito.util.ApplicationNotFoundError: Cannot find fastq-join. Is it installed? Is it in your path?

Based on the above statement I tried to retrieve the required files to the working path. But still it is not working

Please give some clue

Thank you

It is only a problem with the install process, you need to type this in your terminal to install the ea-utils:

sudo apt install ea-utils

Hi Jose Francisco Cobo Diaz,

Thanks a lot for the information. I try and will keep the updates

Hi Jose Francisco Cobo Diaz,,

It worked for me. Thanks a lot

Hi Jayaram, 

Apologies for only getting back to you now. 

But I am glad that your problem has been resolved.

Regards, 

Andries

Hi Andries,

Thank you for the response. I will keep the updates. Once again thank you.

Hi I have one more question.

I have FASTA file with several lacks reads, but the data is demultiplexed. In the title line all terms/words are linked with underscore. I want remove those underscores. How to do that?

>GI-0_M04635:8:000000000AMUGA:1:1101:13602:1821_orig_bc=ACAGAGTCGGCT_new_bc=ACAGAGTCGGCT_bc_diffs=0

>GI-1_M04635:8:000000000AMUGA:1:1101:15756:1852_orig_bc=ACAGAGTCGGCT_new_bc=ACAGAGTCGGCT_bc_diffs=0

but I want the data like this

GI-0 M04635:8:000000000AMUGA:1:1101:13602:1821 orig bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0

>GI-1 M04635:8:000000000AMUGA:1:1101:15756:1852 orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0

The best way is to make your own script to change the names or your sequences (I normally use .gsub() in ruby scripts), because open the file and try to change with the "search and replace" tool of the text editor could be so difficult due to the size of the file. Or... you can split the file (split command in linux shell), change the names in editor and put together again the file with the "cat" command. Or, finally, you can try to use the ".gsub" command in the linux shell, but I don't know how its works, look for any help about this in google and make a prove with a small file to check that its works as you want.

Good luck!!!

Hi,

I currently have the same problem of having fastq-join not installed. Having a MAC, sudo apt doesn't work. I have also tried with brew but didn't manage. Anyone able to help with that?

Thanks

Danilo

Hi Danilo,

Sorry for the delay in response. Please explain the problem. Are you facing problem with qiime scripts or with changing the file format required for qiime.