Training exits prematurely

[gatozee]

FStitch train exists without writing parameter file. Here's the output:

=============================================================
              Fast Read Stitcher Package                     
Last Update: 1/5/2015
Questions? joseph[dot]azofeifa[at]colorado[dot]edu
Running Parameter Estimation

BedGraph File  : sample.min.bedgraph
Training File  : ../trainingSet_minusStrand.txt
Out File       : sample.min.param
Processors     : 8
verbose output : True
=============================================================
reading training file                     : done
making interval tree                      : done
reading bed graph file                    : exiting...

[azofeifa]

so it looks like it is exiting on trying to read the bed graph file. Have you tried specifying the full path to sampleminbedgraph ? cheers, Joey

On Mon, Jan 18, 2016 at 1:54 PM, gatozee notifications@github.com wrote:

FStitch train exists without writing parameter file Here's the output:

          Fast Read Stitcher Package

Last Update: 1/5/2015 Questions? joseph[dot]azofeifa[at]colorado[dot]edu Running Parameter Estimation

BedGraph File : sampleminbedgraph Training File : /trainingSet_minusStrandtxt Out File : sampleminparam Processors : 8

verbose output : True

reading training file : done making interval tree : done reading bed graph file : exiting

— Reply to this email directly or view it on GitHub https://github.com/azofeifa/FStitch/issues/2.

[gatozee]

I tried absolute path, still the same. Didn't FStitch like that file? The bedgraph file was created with bedtools. Can we get more informative error message?

[azofeifa]

yeah I am not sure, the bed graph file should be tab delimitated like this

chromosome[\t]start[\t]stop[\t]coverage[\n]

I don't know how bedtools outputs. you could head the first 1000 lines and I can try running it on my end. If I can figure out the error than I will write some error messages to catch these use cases!

cheers, Joey

On Tue, Jan 19, 2016 at 12:51 PM, gatozee notifications@github.com wrote:

I tried absolute path, still the same. Didn't FStitch like that file? The bedgraph file was created with bedtools. Can we get more informative error message?

— Reply to this email directly or view it on GitHub https://github.com/azofeifa/FStitch/issues/2#issuecomment-172966117.

[gatozee]

Please see the attached bedgraph file. Thanks!

On Tue, Jan 19, 2016 at 3:38 PM, Joey Azofeifa notifications@github.com wrote:

yeah I am not sure, the bed graph file should be tab delimitated like this

chromosome[\t]start[\t]stop[\t]coverage[\n]

I don't know how bedtools outputs. you could head the first 1000 lines and I can try running it on my end. If I can figure out the error than I will write some error messages to catch these use cases!

cheers, Joey

On Tue, Jan 19, 2016 at 12:51 PM, gatozee notifications@github.com wrote:

I tried absolute path, still the same. Didn't FStitch like that file? The bedgraph file was created with bedtools. Can we get more informative error message?

— Reply to this email directly or view it on GitHub https://github.com/azofeifa/FStitch/issues/2#issuecomment-172966117.

— Reply to this email directly or view it on GitHub https://github.com/azofeifa/FStitch/issues/2#issuecomment-172978701.

[azofeifa]

I am not sure the file went through, you might just try emailing it to

jgazofeifa@gmail.com

On Tue, Jan 19, 2016 at 1:41 PM, gatozee notifications@github.com wrote:

Please see the attached bedgraph file. Thanks!

On Tue, Jan 19, 2016 at 3:38 PM, Joey Azofeifa notifications@github.com wrote:

yeah I am not sure, the bed graph file should be tab delimitated like this

chromosome[\t]start[\t]stop[\t]coverage[\n]

I don't know how bedtools outputs. you could head the first 1000 lines and I can try running it on my end. If I can figure out the error than I will write some error messages to catch these use cases!

cheers, Joey

On Tue, Jan 19, 2016 at 12:51 PM, gatozee notifications@github.com wrote:

I tried absolute path, still the same. Didn't FStitch like that file? The bedgraph file was created with bedtools. Can we get more informative error message?

— Reply to this email directly or view it on GitHub https://github.com/azofeifa/FStitch/issues/2#issuecomment-172966117.

— Reply to this email directly or view it on GitHub https://github.com/azofeifa/FStitch/issues/2#issuecomment-172978701.

— Reply to this email directly or view it on GitHub https://github.com/azofeifa/FStitch/issues/2#issuecomment-172979894.

[azofeifa]

Okay, I added some additional error messages although I wasn't able to recover the error on my end, please let me know if it persists. cheers, Joey

On Tue, Jan 19, 2016 at 1:45 PM, Joey Azofeifa <joseph.azofeifa@colorado.edu

wrote:

I am not sure the file went through, you might just try emailing it to

jgazofeifa@gmail.com

On Tue, Jan 19, 2016 at 1:41 PM, gatozee notifications@github.com wrote:

Please see the attached bedgraph file. Thanks!

On Tue, Jan 19, 2016 at 3:38 PM, Joey Azofeifa notifications@github.com wrote:

yeah I am not sure, the bed graph file should be tab delimitated like this

chromosome[\t]start[\t]stop[\t]coverage[\n]

I don't know how bedtools outputs. you could head the first 1000 lines and I can try running it on my end. If I can figure out the error than I will write some error messages to catch these use cases!

cheers, Joey

On Tue, Jan 19, 2016 at 12:51 PM, gatozee notifications@github.com wrote:

I tried absolute path, still the same. Didn't FStitch like that file? The bedgraph file was created with bedtools. Can we get more informative error message?

— Reply to this email directly or view it on GitHub <https://github.com/azofeifa/FStitch/issues/2#issuecomment-172966117 .

— Reply to this email directly or view it on GitHub https://github.com/azofeifa/FStitch/issues/2#issuecomment-172978701.

— Reply to this email directly or view it on GitHub https://github.com/azofeifa/FStitch/issues/2#issuecomment-172979894.