nxtrim: command not found

[robalba1]

Hello,

I am probably missing something obvious here. My NxTrim-0.4.1 install appears to go fine, and I have re-installed it in different locations as a sanity check, but I cannot seem to run what I think is a nxtrim standard run command. For example, if I run:

nxtrim -1 /media/rob/4TB_HD/rawTM_Pcrispum_3.5kb.ACAGTG.L005_1P.fastq.gz -2 /media/rob/4TB_HD/rawTM_Pcrispum_3.5kb.ACAGTG.L005_2P.fastq.gz -O /media/rob/4TB_HD/nxtrim --norc --separate --preservemp-mp

Then the program immediately throws an error: nxtrim: command not found. I am in the NxTrim-0.4.1 directory when I run the command and I can see the nxtrim program (112.5 kB Program file) and the mergeReads program (59.5 kB Program file) in the NxTrim-0.4.1 directory too.

I also get the same error when I try something simple with the example data:

nxtrim -1 /example/MP_R1.fastq.gz -2 /example/MP_R2.fastq.gz -O /home/rob/.linuxbrew/Cellar/NxTrim-0.4.1/example

Again, the program immediately throws an error: nxtrim: command not found.

I have reloaded all my BOOST libraries, so do not think it is a problem with BOOST (as mentioned in a previous "issue."

Any suggestions?

Rob

[odoland]

Try including the path to the Nxtrim. My NxTrim was downloaded and compiled in this directory:
$pwd
/Users/odoland/software/Nxtrim/

I think yours is in /home/rob/.linuxbrew/Cellar/NxTrim-0.4.1/

Then to run it, I would try
$/home/rob/.linuxbrew/Cellar/NxTrim-0.4.1/Nxtrim -1 /example/MP_R1.fastq.gz -2 /example/MP_R2.fastq.gz -O /home/rob/.linuxbrew/Cellar/NxTrim-0.4.1/example

There's a way to run it with just typing Nxtrim. I forget how, but I think it may be using an export PATH command or $cp /home/rob/.linuxbrew/Cellar/NxTrim-0.4.1/Nxtrim /usr/local/bin.

[robalba1]

Thanks odoland. That seemed to help move things forward, but now it throws
another error:

Problem reading
/media/rob/4TB_HD/rawTM_Pcrispum_5-7kb-GCCAAT-L005_1P.fastq.gz.

I have tried to run it with the .fastq file set as well, and it throws the
same error.

Are the dashes ("-") or the underscores ("_") in my file name the issue?

Suggestions?

Rob

On Tue, Jul 19, 2016 at 11:09 AM, odoland notifications@github.com wrote:

Try including the path to the Nxtrim. My NxTrim was downloaded and
compiled in this directory:
$pwd
/Users/odoland/software/Nxtrim/

I think yours is in /home/rob/.linuxbrew/Cellar/NxTrim-0.4.1/

Then to run it, I would try
=/home/rob/.linuxbrew/Cellar/NxTrim-0.4.1/Nxtrim -1 /example/MP_R1.fastq.gz
-2 /example/MP_R2.fastq.gz -O
/home/rob/.linuxbrew/Cellar/NxTrim-0.4.1/example

There's a way to run it with just typing Nxtrim. I forget how, but I think
it may be using an export PATH command or $cp
/home/rob/.linuxbrew/Cellar/NxTrim-0.4.1/Nxtrim /usr/local/bin.

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[odoland]

I don't think the "-" or "_" are the issues. Have you tried NxTrim on the example data set?

I made two bogus files: blah-blah_R1_fastq.gz and blah-blah_R2_fastq.gz
The contents of each file are just:
"Hello World!"

and then Nxtrim -1 blah-blah_R1_fastq.gz -2 blah-blah_R2_fastq.gz was still able to work.. so not the files naming or the contents cause your error.

So I think it could be a permission error with your file? Maybe not allowed access?

I tried the command: (which changes permissions)
$chmod 000 on blahblah.R1.fastq.gz
and I was able to replicate your problem.

"Problem reading: blahblah.R1.fastq.gz"

So maybe try to change permissions:
https://en.wikipedia.org/wiki/Chmod

Try this command: The 777 allows read,write and execute
$chmod 777 /media/rob/4TB_HD/rawTM_Pcrispum_5-7kb-GCCAAT-L005_1P.fastq.gz.

Hope that works!