ERROR: bowtie2 align exited with value 1

Question

[dharris8573]

Hey all,

I am trying to make an appimage for Bowtie2. I don't know if anyone here has experience with appimages but its kind of like a portable app.

I have got it made and it seems to run like this:

And then it errors out with the error in the title.

Anyone have any ideas on how to make this work? Thanks in advanced

if the pics didn't come through here is a link to the album on imgur https://imgur.com/a/XmxKc61

[GenoMax]

How to add images to a Biostars post

Answer 1

[h.mon]

Please do not use images to show error messages, just copy and paste the relevant message and format it using the code button (the button with 101010).

The final error message is explained by the first message from your appimage output:

No index, query, or output file specified!

Which means Bowtie2 is trying to warn your command-line in incomplete.

edit: Bowtie2 provides binary downloads for Linux and MacOs which work on almost all systems, and you can also install it with conda. Why do you want to build an appimage?

[dharris8573]

It's an assignment. I have to run the appimage with the command ./(appimage name) any suggestion on what I need to add to the command to make it work?

[h.mon]

It worked, the error message you got is the same I have running a bowtie2 on a linux system. For example, if instead of just ./Bowtie2.appimage you issue ./Bowtie2.appimage -h, then there should be no error message at the end.

If you want to see if is also working correctly when you pass a complete command line, the use the "example" dataset that comes bundled with both the source and the binary releases of bowtie2. The form of the bowtie2 command is:

bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i>} [-S <sam>]

Read the manual, or if you want a simpler, to-the-point introduction, search for "bowtie2 tutorial".

[dharris8573]

Thanks. But can't even do a full command line after the run command because it immediately closes. Will have to revisit the appimage creation but will keep that command in mind for testing later. Thanks for the help.