BASH stops without error, but works if copied in terminal - bash

Question

I am trying to write a script to slice a 13 Gb file in smaller parts to launch a split computation on a cluster. What I wrote so far works on terminal if I copy and paste it, but stops at the first cycle of the for loop.
set -ueo pipefail
NODES=8
READS=0days_rep2.fasta
Ntot=$(cat $READS | grep 'read' | wc -l)
Ndiv=$(($Ntot/$NODES))
for i in $(seq 0 $NODES)
do
echo $i
start_read=$(cat $READS | grep 'read' | head -n $(($Ndiv*${i}+1)) | tail -n 1)
echo ${start_read}
end_read=$(cat $READS | grep 'read' | head -n $(($Ndiv*${i}+$Ndiv)) | tail -n 1)
echo ${end_read}
done
If I run the script:
(base) [andrea#andrea-xps data]$ bash cluster.sh
0
>baa12ba1-4dc2-4fae-a989-c5817d5e487a runid=314af0bb142c280148f1ff034cc5b458c7575ff1 sampleid=0days_rep2 read=280855 ch=289 start_time=2019-10-26T02:42:02Z
(base) [andrea#andrea-xps data]$
it seems to stop abruptly after the command "echo ${start_read}" without raising any sort of error. If I copy and paste the script in terminal it runs without problems.
I am using Manjaro linux.
Andrea

Answer 1

The problem:
The problem here (as #Jens suggested in a comment) has to do with the use of the -e and pipefail options; -e makes the shell exit immediately if any simple command gets an error, and pipefail makes a pipeline fail if any command in it fails.
But what's failing? Take a look at the command here:
start_read=$(cat $READS | grep 'read' | head -n $(($Ndiv*${i}+1)) | tail -n 1)
Which, clearly, runs the cat, grep, head, and tail commands in a pipeline (which runs in a subshell so the output can be captured and put in the start_read variable). So cat starts up, and starts reading from the file and shoving it down the pipe to grep. grep reads that, picks out the lines containing 'read', and feeds them on toward head. head reads the first line of that (note that on the first pass, Ndiv is 0, so it's running head -n 1) from its input, feeds that on toward the tail command, and then exits. tail passes on the one line it got, then exits as well.
The problem is that when head exited, it hadn't read everything grep had to give it; that left grep trying to shove data into a pipe with nothing on the other end, so the system sent it a SIGPIPE signal to tell it that wasn't going to work, and that caused grep to exit with an error status. And then since it exited, cat was similarly trying to stuff an orphaned pipe, so it got a SIGPIPE as well and also exited with an error status.
Since both cat and grep exited with errors, and pipefail is set, that subshell will also exit with an error status, and that means the parent shell considers the whole assignment command to have failed, and abort the script on the spot.
Solutions:
So, one possible solution is to remove the -e option from the set command. -e is kind of janky in what it considers an exit-worthy error and what it doesn't, so I don't generally like it anyway (see BashFAQ #105 for details).
Another problem with -e is that (as we've seen here) it doesn't give much of any indication of what went wrong, or even that something went wrong! Error checking is important, but so's error reporting.
(Note: the danger in removing -e is that your script might get a serious error partway through... and then blindly keep running, in a situation that doesn't make sense, possibly damaging things in the process. So you should think about what might go wrong as the script runs, and add manual error checking as needed. I'll add some examples to my script suggestion below.)
Anyway, just removing -e is just papering over the fact that this isn't a really good approach to the problem. You're reading (or trying to read) over the entire file multiple times, and processing it through multiple commands each time. You really should only be reading through the thing twice: once to figure out how many reads there are, and once to break it into chunks. You might be able to write a program to do the splitting in awk, but most unix-like systems already have a program specifically for this task: split. There's also no need for cat everywhere, since the other commands are perfectly capable of reading directly from files (again, #Jens pointed this out in a comment).
So I think something like this would work:
#!/bin/bash
set -uo pipefail # I removed the -e 'cause I don't trust it
nodes=8 # Note: lower- or mixed-case variables are safer to avoid conflicts
reads=0days_rep2.fasta
splitprefix=0days_split_
Ntot=$(grep -c 'read' "$reads") || { # grep can both read & count in a single step
# The || means this'll run if there was an error in that command.
# A normal thing to do is print an error message to stderr
# (with >&2), then exit the script with a nonzero (error) status
echo "$0: Error counting reads in $reads" >&2
exit 1
}
Ndiv=$((($Ntot+$nodes-1)/$nodes)) # Force it to round *up*, not down
grep 'read' "$reads" | split -l $Ndiv -a1 - "$splitprefix" || {
echo "$0: Error splitting fasta file" >&2
exit 1
}
This'll create files named "0days_split_a" through "0days_split_h". If you have the GNU version of split, you could add its -d option (use numeric suffixes instead of letters) and/or --additional-suffix=.fasta (to add the .fasta extension to the split files).
Another note: if only a little bit of that big file is read lines, it might be faster to run grep 'read' "$reads" >sometempfile first, and then run the rest of the script on the temp file, so you don't have to read & thin it twice. But if most of the file is read lines, this won't help much.

Answer 2

Alright, we have found the troublemaker: set -e in combination with set -o pipefail.
Gordon Davisson's answer provides all the details. I provide this answer for the sole purpose of reaping an upvote for my debugging efforts in the comments to your answer :-)