No rule to make target error with ABySS-1.3.7 on OS X v10.9.2

[funguy]

Hi,

When I execute this command using the test files:

abyss-pe np=24 name=test k=31 in=‘path_to_file/reads1.fastq path_to_file/reads2.fastq’

I get this error:

make: *** No rule to make target `path_to_file/reads2.fastq’'.  Stop.

this does not see to be a PATH variable problem:

$ which abyss-pe

/usr/local/bin/abyss-pe

I have previously successfully executed abyss-pe on this computer when running v1.3.6 on OS X 10.6.8. Is this a Mavericks issue?

Thanks.

[Ben Vandervalk]

Hi funguy :-)

I usually see that type of error when I've made a typo in the path to the file, or when I have use the -C <working_directory> option with abyss-pe and haven't specified the paths relative to <working_directory>. Other than that, I'm not sure what it could be.

If you type:

$ path_to_file/reads2.fastq

does it show that the file is there?

Have you tried using absolute file paths to see what happens?

Sorry, I am a bit at a loss.

- Ben

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[Ben Vandervalk]

Meant to say

$ ls path_to_file/reads2.fastq

- Ben

[funguy]

Hi Ben,

Thanks for the reply.

Yes, the file shows, so it's not a typo in my path. 

I have an older version of GNU Make (v3.81) -- could this be the issue?

[funguy]

UPDATE****

Seems to be something with the mpirun.

I solved this by

1) changing to the directory where the fastq files were kept and then calling them in the command line using ./

i.e., abyss-pe np=24 name=./FILE_assemblyk31 k=31 in='./FILE_1.fq ./FILE_2.fq'

when I did this, I got a new error:

mpirun -np 24 ABYSS-P -k31 -q3  --coverage-hist=coverage.hist -s FILE_assemblyk31-bubbles.fa  -o FILE_assemblyk31-1.fa ./FILE_1.fq ./FILE_2.fq 

/bin/bash: mpirun: command not found

make: *** [FILE_assemblyk31-1.fa] Error 127

so then I executed abyss-pe without specifying multiple processors (abyss-pe name=./FILE_assemblyk31 k=31 in='./FILE_1.fq ./FILE_2.fq') and it is working.

I have a MacPro with 24 virtual cores and have been able to use them all using ABySS v1.3.6 on OS X 10.6.8.

Any advice?

Thnx

[funguy]

Actually, it was a syntax error in the command.

changing the position of the "k" command to come before the "name" variable solved the problem:

abyss-pe np=24 k=31 name=./FILE_assemblyk31 in='./FILE_1.fq ./FILE_2.fq'

[Tony Raymond]

Hi,

This is quite odd to me. The order of parameters shouldn't matter at all.

I'm wondering if this issue is related to your environment. Please send me the output of the 'env' command, and I'll take a close look.

Thanks,

Tony