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?
-
-
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 -
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 disappearsComment
-
I guess there was never a reply to this problemComment
-
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.--------------
EthanComment
-
I found it was because I hadn't given the -species option, works fine nowComment
-
NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
Comment