I'm encountering the following error when running amosvalidate
brian@Gaff[amos_bank_2] /usr/local/bin/amosvalidate 454Contigs [12:01PM]
The log file is: 454Contigs.runAmos.log
Doing step 100: Creating FastA
Doing step 300: Analyzing mate-pairs
Command: /usr/local/bioinf/Amos/bin/asmQC -b 454Contigs.bnk -scaff -recompute -update -numsd 2 exited with status: 1
Its worked the first time i ran it. however there was no mate pairs info in my bank.
I remade the bank from my newbler assembly and use the xml out put from sff_extract as my matepair info.
Unfortunately, we don't support 454 mates at this time, so I recommend you skip the mate analysis of amosvalidate. Copy the amosvalidate script to a new location:
If you can make this file, you can use any kind of mates you want. Just remember that Amos always expects mates to be of the "innie" variety (pointing towards each other). So you may have to change the orientation of the reads for certain pair library types.
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Hello,
I'm encountering the following error when running amosvalidate
brian@Gaff[amos_bank_2] /usr/local/bin/amosvalidate 454Contigs [12:01PM]
The log file is: 454Contigs.runAmos.log
Doing step 100: Creating FastA
Doing step 300: Analyzing mate-pairs
Command: /usr/local/bioinf/Amos/bin/asmQC -b 454Contigs.bnk -scaff -recompute -update -numsd 2 exited with status: 1
Its worked the first time i ran it. however there was no mate pairs info in my bank.
I remade the bank from my newbler assembly and use the xml out put from sff_extract as my matepair info.
toAmos -ace ../454Contigs.ace -x 454Contigs_traceinfor.xml -o - | bank-transact -m - -b 454Contigs.bnk -c
anyone have any ideas??
regards
Brian
Hi Brian,
Unfortunately, we don't support 454 mates at this time, so I recommend you skip the mate analysis of amosvalidate. Copy the amosvalidate script to a new location:
$ cp /path/to/amos/bin/amosvalidate amosvalidate-nomates
Edit the script to remove the mate analysis by commenting out steps 300-340
## Analyzing mate-pairs
## 300: $(BINDIR)/asmQC -b $(PREF).bnk -scaff -recompute -update -numsd 2
## 310: $(BINDIR)/asmQC -b $(PREF).bnk -scaff -recompute -update -numsd 2
## 320: $(BINDIR)/asmQC -b $(PREF).bnk -scaff -feat -numsd 3 -shortcvg -1 -longcvg -1
## 330: $(BINDIR)/cestat-cov -i -f 4 $(PREF).bnk > $(PREF).ce.feat
## 340: $(BINDIR)/loadFeatures -i $(PREF).bnk $(PREF).ce.feat
Then try the new script
$ amosvalidate-nomates 454Contigs
Good luck!
Michael Schatz
Is this still true? Does Amos not support 454 mates?
You can specify pair information to the toAmos converter using the -m option when you load your reads. This expects a bambus-style mates file: http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus_Manual#The_.mates_file
If you can make this file, you can use any kind of mates you want. Just remember that Amos always expects mates to be of the "innie" variety (pointing towards each other). So you may have to change the orientation of the reads for certain pair library types.