ps: illegal option -- f about aligngraph HOT 6 OPEN

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,
Bao

from aligngraph.

Hi Bao,

well, this is the command I used:
AlignGraph --read1 ORT1breads1.fa --read2 ORT1breads2.fa --contig ORT1b_A5.fa --genome ORT_DSM15997.fa --distanceLow 250 --distanceHigh 1500 --extendedContig ORT1b_A5_extendedContigs.fa --remainingContig ORTb1_A5_remainingContigs.fa

Definitely not coming from my command line input. But if not from AlignGraph itself, were else from? Puzzled...

Best wishes,

Karsten

from aligngraph.

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,
Bao

From: kliere [[email protected]]
Sent: Tuesday, March 24, 2015 1:41 AM
To: baoe/AlignGraph
Cc: Bao
Subject: Re: [AlignGraph] ps: illegal option -- f (#6)

Hi Bao,

well, this is the command I used:
AlignGraph --read1 ORT1breads1.fa --read2 ORT1breads2.fa --contig ORT1b_A5.fa --genome ORT_DSM15997.fa --distanceLow 250 --distanceHigh 1500 --extendedContig ORT1b_A5_extendedContigs.fa --remainingContig ORTb1_A5_remainingContigs.fa

Definitely not coming from my command line input. But if not from AlignGraph itself, were else from? Puzzled...

Best wishes,

Karsten

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/6#issuecomment-85402723.

from aligngraph.

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:
(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 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

from aligngraph.

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,
Bao

From: kliere [[email protected]]
Sent: Friday, March 27, 2015 4:59 AM
To: baoe/AlignGraph
Cc: Bao
Subject: Re: [AlignGraph] ps: illegal option -- f (#6)

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:
(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 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

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/6#issuecomment-86914236.

from aligngraph.

Hi Bao,

Cool - thanks a bunch.

Cheers,

Karsten

from aligngraph.