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Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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OSError: Required binary not found: bowtie2 #94

Closed gh22333 closed 3 years ago

gh22333 commented 4 years ago

Hi, tracer test can't get pass the the bowtie2 not found error. Bowtie2 is in the PATH and is in the tracer.conf file. I tested with bowtie version 2.3.5 and version 2.3.4.3. Thank you for looking into this.

bowtie2_path = /cm/shared/apps/bowtie/2.3.5 bowtie2-build_path = /cm/shared/apps/bowtie/2.3.5

Error: Traceback (most recent call last): File "/cm/shared/apps/tracer/tracer", line 21, in launch() File "/cm/shared/apps/tracer/tracerlib/launcher.py", line 43, in launch Task().run() File "/cm/shared/apps/tracer/tracerlib/tasks.py", line 1224, in run loci=['A', 'B'], max_junc_len=50).run() File "/cm/shared/apps/tracer/tracerlib/tasks.py", line 370, in run self.align() File "/cm/shared/apps/tracer/tracerlib/tasks.py", line 421, in align bowtie2 = self.get_binary('bowtie2') File "/cm/shared/apps/tracer/tracerlib/tasks.py", line 69, in get_binary return check_binary(name, user_path) File "/cm/shared/apps/tracer/tracerlib/io.py", line 156, in check_binary .format(name=name)) OSError: Required binary not found: bowtie2. Please add to PATH or specify location in config file.

Annie

mstubb commented 4 years ago

The entry in your conf file needs to be the path to the binary, not the directory containing the binary. Can you try changing your file and see if it works?

Alternatively, if bowtie2 is in your path you can just comment out those lines in the conf file and it should work.

Let me know if that helps

Mike

On 11 Oct 2019, at 19:31, gh22333 notifications@github.com wrote:

 Hi, tracer test can't get pass the the bowtie2 not found error. Bowtie2 is in the PATH and is in the tracer.conf file. I tested with bowtie version 2.3.5 and version 2.3.4.3. Thank you for looking into this.

bowtie2_path = /cm/shared/apps/bowtie/2.3.5 bowtie2-build_path = /cm/shared/apps/bowtie/2.3.5

Error: Traceback (most recent call last): File "/cm/shared/apps/tracer/tracer", line 21, in launch() File "/cm/shared/apps/tracer/tracerlib/launcher.py", line 43, in launch Task().run() File "/cm/shared/apps/tracer/tracerlib/tasks.py", line 1224, in run loci=['A', 'B'], max_junc_len=50).run() File "/cm/shared/apps/tracer/tracerlib/tasks.py", line 370, in run self.align() File "/cm/shared/apps/tracer/tracerlib/tasks.py", line 421, in align bowtie2 = self.get_binary('bowtie2') File "/cm/shared/apps/tracer/tracerlib/tasks.py", line 69, in get_binary return check_binary(name, user_path) File "/cm/shared/apps/tracer/tracerlib/io.py", line 156, in check_binary .format(name=name)) OSError: Required binary not found: bowtie2. Please add to PATH or specify location in config file.

Annie

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diazdc commented 3 years ago

Hi, I know this issue is a bit dated, but I'm experiencing the same error and my path points directly to both binaries. Both bowtie2 and bowtie2-build are in my PATH. I've verified this using which bowtie2 and which bowtie2-build. I've also tried commenting out both paths in the config file, but that didn't work either. Any help would be appreciated.

mstubb commented 3 years ago

Hi,

@diazdc please can you send me the output of which bowtie2 and also your tracer config file?

Thanks!

Mike

diazdc commented 3 years ago

Hi @mstubb, thanks for getting back to me. This was an error on my part. The binary that wasn't found was for bowtie 1, which I didn't have installed.

mstubb commented 3 years ago

@diazdc - ok, great. Glad you got it worked out!