SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Issues with CASAVA 1.8.1 Orr Shomroni Bioinformatics 19 09-13-2015 04:14 PM
CASAVA 1.7 Install Help aligenie Bioinformatics 29 05-23-2014 03:58 AM
Demultiplexing and CASAVA 1.7 tonio100680 Bioinformatics 14 06-16-2011 11:48 PM
CASAVA installation sehrrot Bioinformatics 1 11-08-2010 05:21 AM
CASAVA, Pipeline 1.3 dvh Illumina/Solexa 19 04-14-2009 09:07 AM

Reply
 
Thread Tools
Old 11-25-2011, 11:27 AM   #1
redindian
Junior Member
 
Location: ny

Join Date: Nov 2011
Posts: 1
Default CASAVA 1.8.2 configureBltoFastq error

Hello to everyone from a new user -I am trying to learn Casava 1.8.2. I am working with a single read 50 bp read and 7bp index run(6 base index--some samples are TruSeq RNA and some lanes have small RNA indices). After running the configureBcltoFastq script I ran make (assuming it does read 1 and read2 for index?). It sttarts but then stops at one of teh lanes giving an error that it "Failed to parse the options:
*** sample-dir not valid: number of directories must match the number of barcodes ***" I did notice that it is reporting all 6 multiplex barcodes and an additional one which it calls undetermined.

Any input? Thanks much!
redindian is offline   Reply With Quote
Old 11-25-2011, 01:16 PM   #2
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 628
Default

Quote:
Originally Posted by redindian View Post
Hello to everyone from a new user -I am trying to learn Casava 1.8.2. I am working with a single read 50 bp read and 7bp index run(6 base index--some samples are TruSeq RNA and some lanes have small RNA indices). After running the configureBcltoFastq script I ran make (assuming it does read 1 and read2 for index?). It sttarts but then stops at one of teh lanes giving an error that it "Failed to parse the options:
*** sample-dir not valid: number of directories must match the number of barcodes ***" I did notice that it is reporting all 6 multiplex barcodes and an additional one which it calls undetermined.

Any input? Thanks much!
How does your sample sheet look like? How did you start configureBcltoFastq?
We need a bit more information ...

cheers,
Sven
sklages is offline   Reply With Quote
Old 07-09-2013, 11:27 PM   #3
dlawrence
Junior Member
 
Location: South Australia

Join Date: Mar 2012
Posts: 8
Default

Quote:
*** sample-dir not valid: number of directories must match the number of barcodes ***"
I just had the same problem.

Short answer: don't put spaces in the SampleSheet.csv fields.

Long answer:

Casava runs in multiple threads causing any errors to be interleaved with debug messages in the log... to work out what lane the problem was, I looked in the Temp directory, and found the one without a XXX_demux_summary.xml file.

In the SampleSheet.csv for that lane I had 5 samples: "Mut F5 Rep1","Mut F5 Rep3" etc. Looking in the lane's directory in Temp/ there was just 1: "Sample_Mut".

So, we've found the source of the error (num directories not equaling num sample sheet samples)

My guess is Casava is not quoting spaces properly in one of the scripts, and this caused the lane samples to overwrite each other, then the directory check failed.

I edited the SampleSheet, changed spaces to dashes, reran and everything was fine. I'll email Illumina and lodge a bug report to fix their quoting.
dlawrence is offline   Reply With Quote
Old 07-09-2013, 11:51 PM   #4
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 628
Default

That is written in "CASAVA v1.8.2 User Guide", p. 31.

We disallowed whitespace and some other characters in sequencing sample names since our first ABI 373 sequencers .. and we still stick to that ;-)
sklages is offline   Reply With Quote
Old 07-10-2013, 12:06 AM   #5
dlawrence
Junior Member
 
Location: South Australia

Join Date: Mar 2012
Posts: 8
Default

Yeah, but it would be good to die immediately with a nice message, not cryptically 15 CPU hours later
dlawrence is offline   Reply With Quote
Old 07-10-2013, 12:45 AM   #6
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 628
Wink

Quote:
Originally Posted by dlawrence View Post
Yeah, but it would be good to die immediately with a nice message, not cryptically 15 CPU hours later
I totally agree, .. but that's the typical UI from Illumina. All of their (unix) software behaves this way; that's partly due to using the 'make' system for processing the data. OLB is funny for error tracking as well ..
sklages is offline   Reply With Quote
Reply

Tags
casava 1.8, hiseq 2000

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:17 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO