RepeatMasker output

flipwell · 04-10-2011, 08:15 PM

Where is the output from RepeatMasker saved? I can see the temporary folder in my directory during running but it disappears when it finishes and I can't find a *.masked file anywhere! Is there a separate option to save the output?

feixue1039 · 04-10-2011, 09:10 PM

Can you find a file named *.log2?
I advise you to check it and make sure that there is no error message in it. Or can you provide the command line you use?

feixue1039

flipwell · 04-10-2011, 09:26 PM

Thanks for your reply - I can't find a *.log2 file either

I ran it as follows: RepeatMasker ../../H99index/H99+mito.fa -lib output_repeats.fa
Then I added the -dir . and some extra output options, -a and -small, to see if that helped, but still nothing. It appears to run fine without throwing any errors, and I can see the files it makes as it runs but when it finishes this all disappears

rfujiwar · 08-17-2011, 07:58 AM

I guess there was never a reply to this problem

ETHANol · 08-17-2011, 08:34 AM

When I run it, it saves the output files to the same directory as the input files are in. So I would guess you have an error along the way.

flipwell · 08-17-2011, 04:48 PM

I found it was because I hadn't given the -species option, works fine now

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04-10-2011, 08:15 PM	#1
flipwell Member Location: Queensland Join Date: Feb 2011 Posts: 14	RepeatMasker output Where is the output from RepeatMasker saved? I can see the temporary folder in my directory during running but it disappears when it finishes and I can't find a *.masked file anywhere! Is there a separate option to save the output?

08-17-2011, 08:34 AM	#5
ETHANol Senior Member Location: Western Australia Join Date: Feb 2010 Posts: 308	When I run it, it saves the output files to the same directory as the input files are in. So I would guess you have an error along the way. __________________ -------------- Ethan

04-10-2011, 09:10 PM	#2
feixue1039 Member Location: China Join Date: Mar 2011 Posts: 18	Can you find a file named *.log2? I advise you to check it and make sure that there is no error message in it. Or can you provide the command line you use? feixue1039

04-10-2011, 09:26 PM	#3
flipwell Member Location: Queensland Join Date: Feb 2011 Posts: 14	Thanks for your reply - I can't find a *.log2 file either I ran it as follows: RepeatMasker ../../H99index/H99+mito.fa -lib output_repeats.fa Then I added the -dir . and some extra output options, -a and -small, to see if that helped, but still nothing. It appears to run fine without throwing any errors, and I can see the files it makes as it runs but when it finishes this all disappears

08-17-2011, 07:58 AM	#4
rfujiwar Junior Member Location: USA Join Date: Oct 2010 Posts: 1	I guess there was never a reply to this problem

08-17-2011, 04:48 PM	#6
flipwell Member Location: Queensland Join Date: Feb 2011 Posts: 14	I found it was because I hadn't given the -species option, works fine now