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Top Forums Shell Programming and Scripting Attach filename to wc results on massive number of files Post 303032281 by bakunin on Thursday 14th of March 2019 02:46:34 PM
Old 03-14-2019
Quote:
Originally Posted by yifangt
The problem with my script is the "echo -n $f" "; always accomplishes first, and the ${f}_R1.fq.gz | wc -l part is behind too much and the result was not aligned as expected.
Actually this is a very interesting problem. It is hard simulate without actually create some terabytes of files that are similar in size to what you have to process, therefore, before i start to actually do that, i'd like to offer a few theories first which you may verify:

my suspicion is that the problem is the buffered nature of <stdout>. From time to time this buffer is flushed and because the output of echo is available already it gets written into the file but since the zcat still runs at that time it will be written at a much later time. Maybe the following might help. I used printf instead of echo, but that is not the point: to execute the output statement the subshell has to be finished, therefore the line should get printed completely or not at all. Because the whole process gets put in background the original order of the filenames will no longer be retained - maybe no concern to you but you should be aware of that.

Another point is the number of processes you start: starting an (in principle unlimited) amount of background processes at the same time is always a bit of an hazard. The script might work well with 10 or 20 files generating 10 or 20 background processes but a directory may as well hold millions of files. No system would survive an attempt to start a million background processes, no matter how small they are and how many processors you have. You may want to implement some logic to only have some maximum number of bround processes running concurrently.

Code:
$(printf "%s\t%s\n" "$f" $(zcat ${f}_R1.fq.gz | wc -l) ) >> raw_reads_count.table1 &

I hope this helps.

bakunin
This User Gave Thanks to bakunin For This Post:
 

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Tcl_DetachPids(3)					      Tcl Library Procedures						 Tcl_DetachPids(3)

__________________________________________________________________________________________________________________________________________________

NAME
Tcl_DetachPids, Tcl_ReapDetachedProcs, Tcl_WaitPid - manage child processes in background SYNOPSIS
#include <tcl.h> Tcl_DetachPids(numPids, pidPtr) Tcl_ReapDetachedProcs() Tcl_Pid Tcl_WaitPid(pid, statusPtr, options) ARGUMENTS
int numPids (in) Number of process ids contained in the array pointed to by pidPtr. int *pidPtr (in) Address of array containing numPids process ids. Tcl_Pid pid (in) The id of the process (pipe) to wait for. int *statusPtr (out) The result of waiting on a process (pipe). Either 0 or ECHILD. int options (in) The options controlling the wait. WNOHANG specifies not to wait when checking the process. _________________________________________________________________ DESCRIPTION
Tcl_DetachPids and Tcl_ReapDetachedProcs provide a mechanism for managing subprocesses that are running in background. These procedures are needed because the parent of a process must eventually invoke the waitpid kernel call (or one of a few other similar kernel calls) to wait for the child to exit. Until the parent waits for the child, the child's state cannot be completely reclaimed by the system. If a parent continually creates children and doesn't wait on them, the system's process table will eventually overflow, even if all the children have exited. Tcl_DetachPids may be called to ask Tcl to take responsibility for one or more processes whose process ids are contained in the pidPtr array passed as argument. The caller presumably has started these processes running in background and does not want to have to deal with them again. Tcl_ReapDetachedProcs invokes the waitpid kernel call on each of the background processes so that its state can be cleaned up if it has exited. If the process has not exited yet, Tcl_ReapDetachedProcs does not wait for it to exit; it will check again the next time it is invoked. Tcl automatically calls Tcl_ReapDetachedProcs each time the exec command is executed, so in most cases it is not necessary for any code outside of Tcl to invoke Tcl_ReapDetachedProcs. However, if you call Tcl_DetachPids in situations where the exec command may never get executed, you may wish to call Tcl_ReapDetachedProcs from time to time so that background processes can be cleaned up. Tcl_WaitPid is a thin wrapper around the facilities provided by the operating system to wait on the end of a spawned process and to check a whether spawned process is still running. It is used by Tcl_ReapDetachedProcs and the channel system to portably access the operating sys- tem. KEYWORDS
background, child, detach, process, wait Tcl Tcl_DetachPids(3)
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