aligning to the reference using CASAVA

kjaja · 10-18-2011, 04:25 PM

Hi,

I have exome sequencing data in zipped fastq format that I am trying to align to the reference using CASAVA. My samples have been sequenced using illumina HiSeq2000 machine, 2 x 100bp paired-end sequencing. The first step in aligning the reads using CASAVA is that I need to create a configureAlignment configuration file. This is my first time using CASAVA so I am not sure how to do that. I was wondering if there is a default setting to align the read to the reference? How to pick what options to use? Can someone provide a sample config.txt file ?

Thanks for your input

GenoMax · 10-19-2011, 05:14 AM

Numbers below refer to lanes. You can analyze all lanes or just one (by eliminating rest of the numbers). Put the text between the lines into "config.txt" (for non-multiplexed samples).

For CASAVA v.1.8
---------------------------------------------
ELAND_FASTQ_FILES_PER_PROCESS 4

USE_BASES Y*,Y*

12345678:ELAND_GENOME /path_to_fasta_reference_files
12345678:ANALYSIS eland_pair
-------------------------------------
Value for the "ELAND_FASTQ_FILES_PER_PROCESS" will need to be adjusted based on the RAM available on the server you are going to run the analysis on.

There are several additional parameters that you can tweak but above example should get you started.

kjaja · 10-19-2011, 02:37 PM

Thanks GenoMax,

In regards to the USE _BASES option, How to determine what bases to ignore when aligning the reads? Is there a rule for that?

GenoMax · 10-20-2011, 04:40 AM

You should not need to ignore any unless you are specifically interested in eliminating some bases from consideration at the beginning/end of the read.

Quote:

Originally Posted by kjaja

Thanks GenoMax,

In regards to the USE _BASES option, How to determine what bases to ignore when aligning the reads? Is there a rule for that?

komais · 07-16-2012, 02:06 AM

I met a error when i use configureAlignment,such as :

config.txt is :
EXPT_DIR /mnt/eql2/liutao/trans/output/Unaligned/
USE_BASES y*,Y*
SAMTOOLS_GENOME /mnt/eql2/my_work_for_now/basic_bio_data/human_ref/hg19/hg19_pure.fa
ANALYSIS eland_pair
OUT_DIR /mnt/eql2/liutao/alignment/Aligned

when i use command line :
/illumina/software/CASAVA-1.8.2/bin/configureAlignment.pl config_new --make

it thrown an error like

[2012-07-16 17:06:25] [configureAlignment.pl] INFO: Running self tests: 'make self_test'

output of 'make self_test':

Makefile:52: Makefiles/config.mk: No such file or directory
make: config.txt config.xml Makefile SampleSheet.csv support.txt No rule to make target `/illumina/software/CASAVA-1.8.2/share/CASAVA-1.8.2/SampleSheet.csv', needed by `Makefiles/config.mk'. Stop.

Self test command exited with error 2 (signal 0)

Investigate and fix errors, then run the command again

[2012-07-16 17:06:25] [configureAlignment.pl] Self test command exited with error 2 (signal 0)
[2012-07-16 17:06:25] [configureAlignment.pl] BACKTRACE: at /illumina/software/CASAVA-1.8.2/lib/CASAVA-1.8.2/perl/Casava/Alignment.pm line 563
Casava::Alignment::selfTest('/mnt/eql2/liutao/alignment/Aligned', 'undef') called at /illumina/software/CASAVA-1.8.2/bin/configureAlignment.pl line 231
Died at /illumina/software/CASAVA-1.8.2/lib/CASAVA-1.8.2/perl/Casava/Common/Log.pm line 310.

If anybody can shed a light for me ??

GenoMax · 07-19-2012, 09:56 AM

Did you run the configureAlignment command while you were in this directory " /mnt/eql2/liutao/trans/output/Unaligned/"? Is there a SampleSheet.mk file in that directory?

Quote:

Originally Posted by komais

I met a error when i use configureAlignment,such as :

config.txt is :
EXPT_DIR /mnt/eql2/liutao/trans/output/Unaligned/
USE_BASES y*,Y*
SAMTOOLS_GENOME /mnt/eql2/my_work_for_now/basic_bio_data/human_ref/hg19/hg19_pure.fa
ANALYSIS eland_pair
OUT_DIR /mnt/eql2/liutao/alignment/Aligned

when i use command line :
/illumina/software/CASAVA-1.8.2/bin/configureAlignment.pl config_new --make

it thrown an error like

[2012-07-16 17:06:25] [configureAlignment.pl] INFO: Running self tests: 'make self_test'

output of 'make self_test':

Makefile:52: Makefiles/config.mk: No such file or directory
make: config.txt config.xml Makefile SampleSheet.csv support.txt No rule to make target `/illumina/software/CASAVA-1.8.2/share/CASAVA-1.8.2/SampleSheet.csv', needed by `Makefiles/config.mk'. Stop.

Self test command exited with error 2 (signal 0)

Investigate and fix errors, then run the command again

[2012-07-16 17:06:25] [configureAlignment.pl] Self test command exited with error 2 (signal 0)
[2012-07-16 17:06:25] [configureAlignment.pl] BACKTRACE: at /illumina/software/CASAVA-1.8.2/lib/CASAVA-1.8.2/perl/Casava/Alignment.pm line 563
Casava::Alignment::selfTest('/mnt/eql2/liutao/alignment/Aligned', 'undef') called at /illumina/software/CASAVA-1.8.2/bin/configureAlignment.pl line 231
Died at /illumina/software/CASAVA-1.8.2/lib/CASAVA-1.8.2/perl/Casava/Common/Log.pm line 310.

If anybody can shed a light for me ??

brojee · 07-07-2019, 07:27 AM

Did you run the configureAlignment order while you were in this catalog "/mnt/eql2/liutao/trans/yield/Unaligned/"? Is there a SampleSheet.mk document in that index?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
aligning the reads	kjaja	Bioinformatics	2	07-07-2019 07:45 AM
Difficulty aligning to reference with AVA	cog	Bioinformatics	8	07-07-2019 07:16 AM
Aligning .fq files	y.divyatej@gmail.com	Illumina/Solexa	0	02-24-2011 04:03 PM
software for aligning ESTs to reference genome	Balat	Bioinformatics	4	07-02-2010 04:50 PM
Aligning contigs w.rt reference sequence	kasutubh	Bioinformatics	7	03-11-2010 12:17 PM

10-18-2011, 04:25 PM	#1
kjaja Member Location: NY Join Date: Aug 2011 Posts: 55	aligning to the reference using CASAVA Hi, I have exome sequencing data in zipped fastq format that I am trying to align to the reference using CASAVA. My samples have been sequenced using illumina HiSeq2000 machine, 2 x 100bp paired-end sequencing. The first step in aligning the reads using CASAVA is that I need to create a configureAlignment configuration file. This is my first time using CASAVA so I am not sure how to do that. I was wondering if there is a default setting to align the read to the reference? How to pick what options to use? Can someone provide a sample config.txt file ? Thanks for your input

10-19-2011, 05:14 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,089	Numbers below refer to lanes. You can analyze all lanes or just one (by eliminating rest of the numbers). Put the text between the lines into "config.txt" (for non-multiplexed samples). For CASAVA v.1.8 --------------------------------------------- ELAND_FASTQ_FILES_PER_PROCESS 4 USE_BASES Y,Y 12345678:ELAND_GENOME /path_to_fasta_reference_files 12345678:ANALYSIS eland_pair ------------------------------------- Value for the "ELAND_FASTQ_FILES_PER_PROCESS" will need to be adjusted based on the RAM available on the server you are going to run the analysis on. There are several additional parameters that you can tweak but above example should get you started. Last edited by GenoMax; 10-19-2011 at 05:25 AM.

07-16-2012, 02:06 AM	#5
komais Junior Member Location: china Join Date: Apr 2011 Posts: 5	I met a error when i use configureAlignment,such as : config.txt is : EXPT_DIR /mnt/eql2/liutao/trans/output/Unaligned/ USE_BASES y,Y SAMTOOLS_GENOME /mnt/eql2/my_work_for_now/basic_bio_data/human_ref/hg19/hg19_pure.fa ANALYSIS eland_pair OUT_DIR /mnt/eql2/liutao/alignment/Aligned when i use command line : /illumina/software/CASAVA-1.8.2/bin/configureAlignment.pl config_new --make it thrown an error like [2012-07-16 17:06:25] [configureAlignment.pl] INFO: Running self tests: 'make self_test' output of 'make self_test': Makefile:52: Makefiles/config.mk: No such file or directory make: config.txt config.xml Makefile SampleSheet.csv support.txt No rule to make target `/illumina/software/CASAVA-1.8.2/share/CASAVA-1.8.2/SampleSheet.csv', needed by `Makefiles/config.mk'. Stop. Self test command exited with error 2 (signal 0) Investigate and fix errors, then run the command again [2012-07-16 17:06:25] [configureAlignment.pl] Self test command exited with error 2 (signal 0) [2012-07-16 17:06:25] [configureAlignment.pl] BACKTRACE: at /illumina/software/CASAVA-1.8.2/lib/CASAVA-1.8.2/perl/Casava/Alignment.pm line 563 Casava::Alignment::selfTest('/mnt/eql2/liutao/alignment/Aligned', 'undef') called at /illumina/software/CASAVA-1.8.2/bin/configureAlignment.pl line 231 Died at /illumina/software/CASAVA-1.8.2/lib/CASAVA-1.8.2/perl/Casava/Common/Log.pm line 310. If anybody can shed a light for me ?? Last edited by komais; 07-16-2012 at 02:08 AM.

07-07-2019, 07:27 AM	#7
brojee Member Location: Bhopal Join Date: Jul 2019 Posts: 19	Did you run the configureAlignment order while you were in this catalog "/mnt/eql2/liutao/trans/yield/Unaligned/"? Is there a SampleSheet.mk document in that index? __________________ Best SEO Company in Bhopal, Best Web Development Company in Bhopal

10-19-2011, 02:37 PM	#3
kjaja Member Location: NY Join Date: Aug 2011 Posts: 55	Thanks GenoMax, In regards to the USE _BASES option, How to determine what bases to ignore when aligning the reads? Is there a rule for that?