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The problem is, the second file does not contain all of the entries in the first file. For those missing I want to leave the second column as zero.

I have two files. One has:


ID# 0 a b c d e f g h i j k....................~2 milion columns
ID# 0 l m n o p q r s t u v....................~2 milion columns
.
.
.
~6000 lines


Other...

Amazing - thanks everyone

sorry to be dumb, but how do I pipe the output from my head -1 command into the echo command?

So, I have a massive file with thousands of columns

I want a list of the headers in one column in another file.

So I need to strip off the top line (can use head-1)

But how can I convert...

That works - great! Thanks!

Is there something hidden at the end of my field that means Non-white wasn't matching then?

Using Linux, I am trying to create a list of all the lines that have "Non-white" or "No" in column 3 of a file: ethnicity.txt.

I have used the following command :

awk '$3 == "No" || $3 ==...

that gives nothing
I am on Linux

maybe I'll just have to wait for the job to finish running, might be done before I go home today :)

I own the files being created
ps -eaf | grep epxlp
gives:
epxlp 15156 29952 0 11:14 pts/7 00:00:00 -bash
epxlp 17349 15156 0 13:36 pts/7 00:00:00 ps -eaf
epxlp 17350...

i dont have the fuser or lsof commands and top doesn't seem to show anything relevant

was using ps aux | grep assoc
Neither this nor your suggestion find anything

also tried searching for my username and can't see the job ps aux | grep epxlp

could it have been renamed by the...

jobs -l produces no output, yet I can see the job is still running as new files are being created all the time

Yesterday I started a nohup job called assoc.sh. It has not finished running, but I have realised a problem with my script, so wish to cancel it, modify and restart it. However, I cannot find the...

When I run the following script:

#! /bin/bash

for var in CA CC CD CT EC PC
do
cat << EOF > ${var}_full.dat
echo T ${var}_high
echo C age
echo C sex
...

Thanks bakunin - the quotes and {} definitely were causing the problem in this instance.

I'll use your tips for my future programming :)

Ok solved it myself. I think.
I needed curly brackets around the variable i within the filename

:)

Ok - I've put some 'echo's in so I could diagnose the problem


1
chrom.mlinfo
chrom.mlprob
./assoc.sh: line 27: 4075 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i...

I've realised the - while [ $i -lt 23 ] - should probably be -lt 22 instead.

However, I'm still getting the same fault message.

Here is the list of errors, --probfile is correct, as I said this command works on its own, just not when in the script.

./assoc.sh: line 24: 31017 Segmentation fault mach2qtl -d PC_full.dat...

Hi I'm very new to this script thing, so please be gentle.

I am trying to get a command - the mach2qtl command in the code below - to loop through a set of files.
Each command should take the...