Program doesn't seem to handle NA as configuration parameter

[galeadmn]

I am currently trying to run the pipeline on a single node, so mode = "LOCAL" in config.py. The config.txt file in the project directory contains NA on several lines, for example:
trimgalore NA/NA/NA

I get the following runtime error when I try to run the pipeline:

Traceback (most recent call last):
File "/share/aRNAPipe/code/lib/wr_aRNApipe.py", line 181, in
if int(var["trimgalore"].split("/")[0]) > 0:
ValueError: invalid literal for int() with base 10: 'NA'

I do not see anywhere in the code where the program checks to see if the parameter input is 'NA'. Am I missing something?

[blasseigne]

Hello, Can you confirm what version of aRNApipe you are using and provide the full config file? One note, if you do not want to run trimgalore, it should be '0/NA/NA' instead of 'NA/NA/NA'. https://github.com/HudsonAlpha/aRNAPipe/wiki/2.-aRNApipe:-The-main-application#config Thanks Brittany N. Lasseigne, Ph.D. Senior Scientist, Myers Lab HudsonAlpha Institute for Biotechnology 601 Genome Way Huntsville, Alabama 35806

…

On Tue, Dec 12, 2017 at 12:21 PM, galeadmn ***@***.***> wrote: I am currently trying to run the pipeline on a single node, so mode = "LOCAL" in config.py. The config.txt file in the project directory contains NA on several lines, for example: trimgalore NA/NA/NA I get the following runtime error when I try to run the pipeline: Traceback (most recent call last): File "/share/aRNAPipe/code/lib/wr_aRNApipe.py", line 181, in if int(var["trimgalore"].split("/")[0]) > 0: ValueError: invalid literal for int() with base 10: 'NA' I do not see anywhere in the code where the program checks to see if the parameter input is 'NA'. Am I missing something? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#10>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGL5tv5rIRrkGezYTlho_QH2ky0NfLYHks5s_sQfgaJpZM4Q_a8K> .

[galeadmn]

Hi Brittany, I believe that I made a mistake. I realized later that NA is not allowed in the first position and that it must be a number. Is there a forum where questions about aRNAPipe can be posted? I used the github wiki because I didn’t know where else to seek help. Thank you, Frank From: Brittany N. Lasseigne, PhD [mailto:[email protected]] Sent: Thursday, December 14, 2017 7:16 AM To: HudsonAlpha/aRNAPipe <[email protected]> Cc: galeadmn <[email protected]>; Author <[email protected]> Subject: Re: [HudsonAlpha/aRNAPipe] Program doesn't seem to handle NA as configuration parameter (#10) Hello, Can you confirm what version of aRNApipe you are using and provide the full config file? One note, if you do not want to run trimgalore, it should be '0/NA/NA' instead of 'NA/NA/NA'. https://github.com/HudsonAlpha/aRNAPipe/wiki/2.-aRNApipe:-The-main-application#config Thanks Brittany N. Lasseigne, Ph.D. Senior Scientist, Myers Lab HudsonAlpha Institute for Biotechnology 601 Genome Way Huntsville, Alabama 35806

On Tue, Dec 12, 2017 at 12:21 PM, galeadmn ***@***.******@***.***>> wrote: I am currently trying to run the pipeline on a single node, so mode = "LOCAL" in config.py. The config.txt file in the project directory contains NA on several lines, for example: trimgalore NA/NA/NA I get the following runtime error when I try to run the pipeline: Traceback (most recent call last): File "/share/aRNAPipe/code/lib/wr_aRNApipe.py", line 181, in if int(var["trimgalore"].split("/")[0]) > 0: ValueError: invalid literal for int() with base 10: 'NA' I do not see anywhere in the code where the program checks to see if the parameter input is 'NA'. Am I missing something? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#10>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGL5tv5rIRrkGezYTlho_QH2ky0NfLYHks5s_sQfgaJpZM4Q_a8K> .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#10 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AePh79ksZuCZk5iPOwRc8J4LMHQUfcaKks5tATu8gaJpZM4Q_a8K>.

[blasseigne]

Hi Frank, For the time being issue tickets on GitHub are the best way to reach out. Thanks, Brittnay Brittany N. Lasseigne, Ph.D. Senior Scientist, Myers Lab HudsonAlpha Institute for Biotechnology 601 Genome Way Huntsville, Alabama 35806

…

On Thu, Dec 14, 2017 at 1:29 PM, galeadmn ***@***.***> wrote: Hi Brittany, I believe that I made a mistake. I realized later that NA is not allowed in the first position and that it must be a number. Is there a forum where questions about aRNAPipe can be posted? I used the github wiki because I didn’t know where else to seek help. Thank you, Frank From: Brittany N. Lasseigne, PhD ***@***.*** Sent: Thursday, December 14, 2017 7:16 AM To: HudsonAlpha/aRNAPipe ***@***.***> Cc: galeadmn ***@***.***>; Author ***@***.***> Subject: Re: [HudsonAlpha/aRNAPipe] Program doesn't seem to handle NA as configuration parameter (#10) Hello, Can you confirm what version of aRNApipe you are using and provide the full config file? One note, if you do not want to run trimgalore, it should be '0/NA/NA' instead of 'NA/NA/NA'. https://github.com/HudsonAlpha/aRNAPipe/wiki/2.-aRNApipe:-The-main- application#config Thanks Brittany N. Lasseigne, Ph.D. Senior Scientist, Myers Lab HudsonAlpha Institute for Biotechnology 601 Genome Way Huntsville, Alabama 35806 On Tue, Dec 12, 2017 at 12:21 PM, galeadmn ***@***.***< ***@***.***>> wrote: > I am currently trying to run the pipeline on a single node, so mode = > "LOCAL" in config.py. The config.txt file in the project directory contains > NA on several lines, for example: > trimgalore NA/NA/NA > > I get the following runtime error when I try to run the pipeline: > > Traceback (most recent call last): > File "/share/aRNAPipe/code/lib/wr_aRNApipe.py", line 181, in > if int(var["trimgalore"].split("/")[0]) > 0: > ValueError: invalid literal for int() with base 10: 'NA' > > I do not see anywhere in the code where the program checks to see if the > parameter input is 'NA'. Am I missing something? > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#10>, or mute the thread > <https://github.com/notifications/unsubscribe-auth/AGL5tv5rIRrkGezYTlho_ QH2ky0NfLYHks5s_sQfgaJpZM4Q_a8K> > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://github.com/ HudsonAlpha/aRNAPipe#10#issuecomment-351739725>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ AePh79ksZuCZk5iPOwRc8J4LMHQUfcaKks5tATu8gaJpZM4Q_a8K>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGL5tsO41XIvkzIOMWHmgwjkovU2L3spks5tAXcJgaJpZM4Q_a8K> .