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ps: illegal option -- f #6
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Hi, Karsten, AlignGraph does not have this warning message, and it looks like you inputted a Linux command line with "ps --f" right after AlignGraph's command. Maybe you can double check the command lines you inputted with/without rerunning AlignGraph (since it looks the AlignGraph run does not take much time)? Best, |
Hi Bao, well, this is the command I used: Definitely not coming from my command line input. But if not from AlignGraph itself, were else from? Puzzled... Best wishes, Karsten |
Hi, Karsten, I guess it comes from a second command line following the AlignGraph command line. It could be a misinput during AlignGraph's running. I'd suggest you to rerun AlignGraph and see if the problem can disappear, since it only takes 3192 seconds in total according to the printout you sent me. Best, From: kliere [notifications@github.com] Hi Bao, well, this is the command I used: Definitely not coming from my command line input. But if not from AlignGraph itself, were else from? Puzzled... Best wishes, Karsten — |
Hi Bao, now that we are talking about it - I just recalled that I used AlignGraph on my Mac. That might explain the error, which does consistently come up: (0) Alignment finished CHROMOSOME 0: FINISHED for 3181 seconds (1741 seconds for alignment) :-) I tried running it on my Linux box before. However, due to restricted disc space (I presume), the process gets killed at step (2) contig alignment loaded. Therefore, I tried it on my Mac... Maybe compiling AlignGraph on the Mac will solve this error? What do you think? Best wishes, Karsten |
Hi, Karsten, Finally, I got the reason: I have a line in the source code calling a Linux command "system("ps euf >> mem.txt");", but it failed since it was run on Mac. However, don't worry about the failure, because this command only outputs memory usage and has nothing to do with the final results. Hope this helps. Best, From: kliere [notifications@github.com] Hi Bao, now that we are talking about it - I just recalled that I used AlignGraph on my Mac. That might explain the error, which does consistently come up: (0) Alignment finished CHROMOSOME 0: FINISHED for 3181 seconds (1741 seconds for alignment) :-) I tried running it on my Linux box before. However, due to restricted disc space (I presume), the process gets killed at step (2) contig alignment loaded. Therefore, I tried it on my Mac... Maybe compiling AlignGraph on the Mac will solve this error? What do you think? Best wishes, Karsten — |
Hi Bao, Cool - thanks a bunch. Cheers, Karsten |
Hi,
I get this messages while running AlignGraph:
(0) Alignment finished
CHROMOSOME 0:
(1) chromosome loaded
(2) contig alignment loaded
(3) read alignment loaded
(4) contigs extended
(5) contigs scaffolded
ps: illegal option -- f
usage: ps [-AaCcEefhjlMmrSTvwXx] [-O fmt | -o fmt] [-G gid[,gid...]]
[-u]
[-p pid[,pid...]] [-t tty[,tty...]] [-U user[,user...]]
ps [-L]
FINISHED for 3192 seconds (2064 seconds for alignment) :-)
What does this ps error mean and how to get around it?
Best wishes,
Karsten
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