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mhammell-laboratory / TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
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Can not run TEtranscripts with test files. #4

Closed jdaron closed 8 years ago

jdaron commented 8 years ago

Hello,

I am contacting you because I just install TEtranscripts and all the dependency to my computer, and I was unsuccessful to launch TEtranscripts with the test files you are providing.

Here is the error message I got: INFO @ Wed, 02 Dec 2015 18:20:21: Finished processing sample files INFO @ Wed, 02 Dec 2015 18:20:21: Generating counts table CRITICAL @ Wed, 02 Dec 2015 18:20:21: Error in running differential analysis!

CRITICAL @ Wed, 02 Dec 2015 18:20:21: Error: [Errno 13] Permission denied

CRITICAL @ Wed, 02 Dec 2015 18:20:21: [Exception type: OSError, raised in subprocess.py:1335]

Here if the commend line I am launching: $ TEtranscripts --sortByPos --mode multi --TE dm3_rmsk_TE.gtf --GTF dm3_refGene.gtf --project singleEnd_test -t test_data_SE_treatment.bam -c test_data_SE_control.bam 2> log

To provide you information on my environment I I install pysam correctly : $ pip install pysam Requirement already satisfied (use --upgrade to upgrade): pysam in /Users/daron.6/Library/Python/3.4/lib/python/site-packages Requirement already satisfied (use --upgrade to upgrade): cython>=0.20.1 in /Users/daron.6/Library/Python/3.4/lib/python/site-packages (from pysam)

And I install DESeq using the following command: source("http://www.bioconductor.org/biocLite.R") biocLite("DESeq")

Thanks for helping me to figure out a way to make the program working. Josquin

molikd commented 8 years ago

From: Daron, Josquin M. [daron.6@osu.edu] Sent: Thursday, December 03, 2015 3:49 PM To: Jin, Ying Subject: Re: problem when running TEtranscripts with test files

Hi Thanks a lot for your quick answer,

So I do have the correct *.cntTabe and *.R. I run the Rscript in a R session and it seams that everything goes well. I got 2 file singleEnd_test_gene_TE_analysis.txt and singleEnd_test_sigdiff_gene_TE.txt. I think the problem is in my imac I only have a R.app, which I am using with Rstudio. But I don’t access to this R.app in the terminal, and they is no R in my usr/bin/. So I create a symbolic link between where is located Rscript in my computer and my bin, and it works: Here is the cmd: ln -s /Library/Frameworks/R.framework/Resources/bin/Rscript ~/bioInf/bin/.

Thanks for your help, it was really useful. Best, Josquin

On Dec 3, 2015, at 2:35 PM, Jin, Ying yjin@cshl.edu wrote:

Hi, Thanks for your interests in TEtranscripts.

It seem like there is an issue of running Rscript. Can you please check in your output folder whether there is a file named _*.cntTable, it contains the gene/TE abundance estimation values, and also wether there is a file name _.R, it is a Rscript to run DESeq on the .cntTable? If there are those files, can you just run Rscript **.R from your command line and to see whether it can go through or not?

Best, Ying

Ying Jin PhD

Bioinformatics Shared Resources Cold Spring Harbor Lab 516-367-5190 yjin at cshl dot edu

From: Daron, Josquin M. [daron.6@osu.edu] Sent: Thursday, December 03, 2015 1:59 PM To: Jin, Ying Subject: problem when running TEtranscripts with test files

Hello,

I am contacting you because I just install TEtranscripts and all the dependency to my computer, and I was unsuccessful to launch TEtranscripts with the test files you are providing.

Here is the error message I got: INFO @ Wed, 02 Dec 2015 18:20:21: Finished processing sample files INFO @ Wed, 02 Dec 2015 18:20:21: Generating counts table CRITICAL @ Wed, 02 Dec 2015 18:20:21: Error in running differential analysis!

CRITICAL @ Wed, 02 Dec 2015 18:20:21: Error: [Errno 13] Permission denied

CRITICAL @ Wed, 02 Dec 2015 18:20:21: [Exception type: OSError, raised in subprocess.py:1335]

Here if the commend line I am launching: $ TEtranscripts --sortByPos --mode multi --TE dm3_rmsk_TE.gtf --GTF dm3_refGene.gtf --project singleEnd_test -t test_data_SE_treatment.bam -c test_data_SE_control.bam 2> log

To provide you information on my environment I I install pysam correctly : $ pip install pysam Requirement already satisfied (use --upgrade to upgrade): pysam in /Users/daron.6/Library/Python/3.4/lib/python/site-packages Requirement already satisfied (use --upgrade to upgrade): cython>=0.20.1 in /Users/daron.6/Library/Python/3.4/lib/python/site-packages (from pysam)

And I install DESeq using the following command: source("http://www.bioconductor.org/biocLite.R") biocLite("DESeq")

Lastly I should add that I am using Python 2.7.10.

Thanks for helping me to figure out a way to make the program working. Josquin

molikd commented 8 years ago

Marking Resolved.