I am working with data from MiSeq bcl files, I want to convert it to fastq files using the bcl2fastq.
below is sample of my data
[Header]
IEMFileVersion 4
Investigator Name XXXXX
Experiment Name XXXX_plate01_1pool
Date xx/xx/xxxx
Workflow GenerateFASTQ
Application FASTQ Only
Assay TruSeq LT
Description Test
Chemistry Default
Reads
250
250
[Settings]
ReverseComplement 0
Adapter TTTTTTTTTTTTTTT
AdapterRead2 AAAAAAAAAAAA
[Data]
FCID Lane SampleID Sample_Ref index Description Control Recipe Operator Sample_Project
073388Sm XXXXXXXX
073389Sm XXXXXXXX
073390Sm XXXXXXXX
073391Sm XXXXXXXX
073392Sm XXXXXXXX
073393Sm XXXXXXXX
073394Sm XXXXXXXX
cont1 XXXXXXXX
bash-4.1$ /home/Downloads/CASAVA/bin/configureBclToFastq.pl --output-dir /home/Projects/Data/unaligned --input-dir /home/Projects/Data/Intensities/BaseCalls --fastq-cluster-count 0 --sample-sheet /home/Projects/Data/Intensities/BaseCalls/SampleSheet.csv --tiles s_1_* --force --mismatches 1 --ignore-missing-bcl --ignore-missing-stats --use-bases-mask n
could not find ParserDetails.ini in /home/Downloads/localperl/lib/site_perl/5.20.2/XML/SAX
[2015-02-24 17:18:02] [configureBclToFastq.pl] INFO: Basecalling software: RTA
[2015-02-24 17:18:02] [configureBclToFastq.pl] INFO: version: 1.18 (build 54)
[2015-02-24 17:18:02] [configureBclToFastq.pl] WARNING: Couldn't find run info in /home/Projects/Data/Intensities/BaseCalls/../../../RunInfo.xml
[2015-02-24 17:18:02] [configureBclToFastq.pl] WARNING: Couldn't find RunInfo.xml for /home/Projects/Data/Intensities/BaseCalls
[2015-02-24 17:18:02] [configureBclToFastq.pl] INFO: Original use-bases mask: n
[2015-02-24 17:18:02] [configureBclToFastq.pl] INFO: Guessed use-bases mask: n
ERROR: Wrong number of fields in sample sheet (expected: 10, got 8: IEMFileVersion,4,,,,,,)
at /home/Downloads/CASAVA/lib/bcl2fastq-1.8.4/perl/Casava/Demultiplex.pm line 531
I am running casava for the first time so any help will be appreciated
Thank you
below is sample of my data
[Header]
IEMFileVersion 4
Investigator Name XXXXX
Experiment Name XXXX_plate01_1pool
Date xx/xx/xxxx
Workflow GenerateFASTQ
Application FASTQ Only
Assay TruSeq LT
Description Test
Chemistry Default
Reads
250
250
[Settings]
ReverseComplement 0
Adapter TTTTTTTTTTTTTTT
AdapterRead2 AAAAAAAAAAAA
[Data]
FCID Lane SampleID Sample_Ref index Description Control Recipe Operator Sample_Project
073388Sm XXXXXXXX
073389Sm XXXXXXXX
073390Sm XXXXXXXX
073391Sm XXXXXXXX
073392Sm XXXXXXXX
073393Sm XXXXXXXX
073394Sm XXXXXXXX
cont1 XXXXXXXX
bash-4.1$ /home/Downloads/CASAVA/bin/configureBclToFastq.pl --output-dir /home/Projects/Data/unaligned --input-dir /home/Projects/Data/Intensities/BaseCalls --fastq-cluster-count 0 --sample-sheet /home/Projects/Data/Intensities/BaseCalls/SampleSheet.csv --tiles s_1_* --force --mismatches 1 --ignore-missing-bcl --ignore-missing-stats --use-bases-mask n
could not find ParserDetails.ini in /home/Downloads/localperl/lib/site_perl/5.20.2/XML/SAX
[2015-02-24 17:18:02] [configureBclToFastq.pl] INFO: Basecalling software: RTA
[2015-02-24 17:18:02] [configureBclToFastq.pl] INFO: version: 1.18 (build 54)
[2015-02-24 17:18:02] [configureBclToFastq.pl] WARNING: Couldn't find run info in /home/Projects/Data/Intensities/BaseCalls/../../../RunInfo.xml
[2015-02-24 17:18:02] [configureBclToFastq.pl] WARNING: Couldn't find RunInfo.xml for /home/Projects/Data/Intensities/BaseCalls
[2015-02-24 17:18:02] [configureBclToFastq.pl] INFO: Original use-bases mask: n
[2015-02-24 17:18:02] [configureBclToFastq.pl] INFO: Guessed use-bases mask: n
ERROR: Wrong number of fields in sample sheet (expected: 10, got 8: IEMFileVersion,4,,,,,,)
at /home/Downloads/CASAVA/lib/bcl2fastq-1.8.4/perl/Casava/Demultiplex.pm line 531
I am running casava for the first time so any help will be appreciated
Thank you
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