HPC:bclconvert
From HPC wiki
BCL Convert
The Illumina BCL Convert is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina™ sequencing systems to FASTQ files. Additionally, BCL Convert provides adapter handling (through masking and trimming) and UMI trimming and produces metric outputs.
BCL Convert module usage
To check available versions of BCL Convert, run the "module avail" command:
[asrini@node155 ~]$ module avail --------------------------------------------------------------------------------- /usr/share/Modules/modulefiles ---------------------------------------------------------------------------------- AllPaths-LG-v49967 bzip2/1.0.6 gcc/8.3.1 NAMD-2.9-Linux-x86_64-multicore R/3.1.1 samtools-1.1 autoconf/2.69 CASAVA/v1.8.2 gsl-2.1 ngsutils-0.5.7 R/3.1.2 scons/2.3.1 automake/1.15 cellranger/5.0.1 hdf5/1.8.21 null R/3.2.1 SOAPdenovo2-r240 bamtools/2.3.0 circos/0.67-5 homer-v4.6 pandoc/2.0.6 R/3.2.2 STAR/2.3.0e bcftools/1.11 cmake/3.21.1 htslib/1.11 pandoc/2.3 R/3.3.0 STAR/2.4.1d bcl2fastq2/v2.15.0.4 cufflinks-2.2.0 java/openjdk-1.6.0 parallel/20201122 R/3.3.1 STAR/2.5.2a bcl2fastq2/v2.16.0.10 cufflinks-2.2.1 java/openjdk-1.7.0 pcre-8.38 R/3.4.2 STAR/2.7.1a bcl2fastq2/v2.17.1.14 curl-7.49.0 java/openjdk-1.8.0 perl5lib R/3.4.3 texinfo/6.0 bcl2fastq2/v2.19.0.316 dot julia/1.0.5 picard/1.96 R/3.5.1 texlive-20170214 bcl2fastq2/v2.20.0.422 EMBOSS-6.6.0 julia/1.4.2 picard-tools-1.141 R/3.6.3 Trimmomatic-0.32 bcl-convert/3.8.2 eQtlBma-1.2.2 ld-library-path pkg-config-path R/4.0.2 trinity-r20140717 blat-v35 eQtlBma-1.3.1 libtool/2.4.6 plink-1.90b3b rclone/1.47.0 use.own boost/1.55.0 FastQC-0.11.2 local_coreutils-8.24 python/2.7.9 RUM/2.0.5_06 wget/1.20.3 boost/1.57.0 fastx_toolkit-0.0.14 manpath python/3.6.3 sailfish/0.6.3 WiggleTools/1.0 bowtie2/2.1.0 gcc/5.3.1 module-git python/3.9.1 samtools/1.11 zlib/1.2.8 bowtie2/2.3.4.1 gcc/6.3.1 module-info qiime/1.8.0 samtools-0.1.18 bwa-0.7.10 gcc/7.3.1 modules QTLtools/1.3.1-11 samtools-0.1.19 ---------------------------------------------------------------------------------------- /etc/modulefiles ----------------------------------------------------------------------------------------- mpi/mpich-3.0-x86_64 mpi/mpich-3.2-x86_64 mpi/mpich-x86_64
To load/use one of the available BCL Convert modules run the "module load" command (click "expand" to see basic module usage):
[asrini@node155 ~]$ module load bcl-convert/3.8.2
[asrini@node155 ~]$ which bcl-convert
/opt/software/bcl-convert/3.8.2/bin/bcl-convert
[asrini@node155 ~]$ bcl-convert
bcl-convert Version 00.000.000.3.8.2-12-g85770e0b
Copyright (c) 2014-2018 Illumina, Inc.
Run BCL Conversion (BCL directory to *.fastq.gz)
bcl-convert --bcl-input-directory <BCL_ROOT_DIR> --output-directory <PATH> [options]
Options:
-h [ --help ] Print this help message
-V [ --version ] Print the version and exit
--output-directory arg Output BCL directory for BCL conversion (must be specified)
-f [ --force ] Force: allow destination diretory to already exist
--bcl-input-directory arg Input BCL directory for BCL conversion (must be specified)
--sample-sheet arg Path to SampleSheet.csv file (default searched for in --bcl-input-directory)
--bcl-only-lane arg Convert only specified lane number (default all lanes)
--strict-mode arg Abort if any files are missing (false by default)
--first-tile-only arg Only convert first tile of input (for testing & debugging)
--bcl-sampleproject-subdirectories arg Output to subdirectories based upon sample sheet 'Sample_Project' column
--shared-thread-odirect-output arg Use linux native asynchronous io (io_submit) for file output (Default=false)
--bcl-num-parallel-tiles arg # of tiles to process in parallel (default 1)
--bcl-num-conversion-threads arg # of threads for conversion (per tile, default # cpu threads)
--bcl-num-compression-threads arg # of threads for fastq.gz output compression (per tile, default # cpu threads,
or HW+12)
--bcl-num-decompression-threads arg # of threads for bcl/cbcl input decompression (per tile, default half # cpu
threads, or HW+8. Only applies when preloading files)
--no-lane-splitting arg Do not split FASTQ file by lane (false by default)
[asrini@node155 ~]$ bcl-convert -V
bcl-convert Version 00.000.000.3.8.2-12-g85770e0b
Copyright (c) 2014-2018 Illumina, Inc.
