install bcl2fastq

Question

[yueli7]

Hello,

I tried to install bcl2fastq in my Ubuntu Ubuntu 18.04.3 LTS.

1. Is the installation correct, even it has error Unable to open '/home/li/RunInfo.xml' file for reading?

2. If I want to use bcl2fastq, I have to type./usr/local/bin/bcl2fastq.

Which command that I can use bcl2fastq in any of the terminal, and do not need to type ./usr/local/bin/bcl2fastq again and again?

Thanks in advance for any suggestions!

Best,

Yue

li@li-HP-Pavilion-Desktop-590-p0xxx:~$ ./usr/local/bin/bcl2fastq
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.

2020-02-04 17:22:08 [1f53880] Command-line invocation: ./usr/local/bin/bcl2fastq 
2020-02-04 17:22:08 [1f53880] INFO: Minimum log level: INFO
2020-02-04 17:22:08 [1f53880] INFO: Sample sheet: '/home/li/SampleSheet.csv'
2020-02-04 17:22:08 [1f53880] INFO: Sample sheet: NOT FOUND
2020-02-04 17:22:08 [1f53880] INFO: Runfolder path: '/home/li'
2020-02-04 17:22:08 [1f53880] INFO: Input path: '/home/li/Data/Intensities/BaseCalls/'
2020-02-04 17:22:08 [1f53880] INFO: Intensities path: '/home/li/Data/Intensities/'
2020-02-04 17:22:08 [1f53880] INFO: Output path: '/home/li/Data/Intensities/BaseCalls/'
2020-02-04 17:22:08 [1f53880] INFO: InterOp path: '/home/li/InterOp/'
2020-02-04 17:22:08 [1f53880] INFO: Stats path: '/home/li/Data/Intensities/BaseCalls/Stats/'
2020-02-04 17:22:08 [1f53880] INFO: Reports path: '/home/li/Data/Intensities/BaseCalls/Reports/'
2020-02-04 17:22:08 [1f53880] INFO: Detected CPUs: 12
2020-02-04 17:22:08 [1f53880] INFO: Loading threads: 4
2020-02-04 17:22:08 [1f53880] INFO: Processing threads: 12
2020-02-04 17:22:08 [1f53880] INFO: Writing threads: 4
2020-02-04 17:22:08 [1f53880] INFO: Allowed barcode mismatches: 1 
2020-02-04 17:22:08 [1f53880] INFO: Tiles: <ALL>
2020-02-04 17:22:08 [1f53880] INFO: Minimum trimmed read length: 35
2020-02-04 17:22:08 [1f53880] INFO: Use bases masks: <NONE>
2020-02-04 17:22:08 [1f53880] INFO: Mask short adapter reads: 22
2020-02-04 17:22:08 [1f53880] INFO: Adapter stringency: 0.9
2020-02-04 17:22:08 [1f53880] INFO: Adapter trimming method: Allow matches with indels
2020-02-04 17:22:08 [1f53880] INFO: Ignore missing BCLs: NO
2020-02-04 17:22:08 [1f53880] INFO: Ignore missing filters: NO
2020-02-04 17:22:08 [1f53880] INFO: Ignore missing positions: NO
2020-02-04 17:22:08 [1f53880] INFO: Ignore missing controls: NO
2020-02-04 17:22:08 [1f53880] INFO: Include non-PF clusters: NO
2020-02-04 17:22:08 [1f53880] INFO: Create FASTQs for index reads: NO
2020-02-04 17:22:08 [1f53880] INFO: Use bgzf compression for FASTQ files: YES
2020-02-04 17:22:08 [1f53880] INFO: FASTQ compression level: 4
2020-02-04 17:22:08 [1f53880] INFO: RunInfo.xml: '"/home/li/RunInfo.xml"'
2020-02-04 17:22:08 [1f53880] ERROR: bcl2fastq::common::Exception: 2020-Feb-04 17:22:08: No such file or directory (2): /TeamCityBuildAgent/work/556afd631a5b66d8/src/cxx/lib/io/Xml.cpp(201): Throw in function boost::property_tree::ptree bcl2fastq::io::parseXmlFile(const boost::filesystem::path&)
Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::IoError>
std::exception::what: Unable to open '/home/li/RunInfo.xml' file for reading

[sklages]

The first question: just use bcl2fastq --help to avoid this error message. bcl2fastq without any arguments assumes the current working directory to be a valid run folder (See: INFO: Runfolder path: '/home/li').

[yueli7]

Hello, sklages,

Thank you so much for your great help! It works!

How I can use export command to let bcl2fastq run in any terminal. My home folder is /home/li/

Thank you in advance for your great help!

Best,

Yue

li@li-HP-Pavilion-Desktop-590-p0xxx:~$ ./usr/local/bin/bcl2fastq --help
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.

Usage:
  bcl2fastq [options]

li@li-HP-Pavilion-Desktop-590-p0xxx:~$ export PATH="./usr/local/bin/bcl2fastq:$PATH"
li@li-HP-Pavilion-Desktop-590-p0xxx:~$ ./bcl2fastq --help
bash: ./bcl2fastq: Is a directory

li@li-HP-Pavilion-Desktop-590-p0xxx:~$ export PATH="./usr/local/bin/bcl2fastq:$/home/li/"
li@li-HP-Pavilion-Desktop-590-p0xxx:~$ ./bcl2fastq --help
bash: ./bcl2fastq: Is a directory

[colindaven]

For the second question, you need to add bcl2fastq to your PATH, eg something like

https://askubuntu.com/questions/60218/how-to-add-a-directory-to-the-path

[yueli7]

Hello, colindaven,

Thank you so much for your great help!

How I can use export command to let bcl2fastq run in any terminal. My home folder is /home/li/.

Thank you in advance for your great help!

Best,

Yue

li@li-HP-Pavilion-Desktop-590-p0xxx:~$ ./usr/local/bin/bcl2fastq --help
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.

Usage:
  bcl2fastq [options]

li@li-HP-Pavilion-Desktop-590-p0xxx:~$ export PATH="./usr/local/bin/bcl2fastq:$PATH"
li@li-HP-Pavilion-Desktop-590-p0xxx:~$ ./bcl2fastq --help
bash: ./bcl2fastq: Is a directory

li@li-HP-Pavilion-Desktop-590-p0xxx:~$ export PATH="./usr/local/bin/bcl2fastq:$/home/li/"
li@li-HP-Pavilion-Desktop-590-p0xxx:~$ ./bcl2fastq --help
bash: ./bcl2fastq: Is a directory

[colindaven]

Try creating a file like this globalenv and adding it to your /home/YOURUSER/.bashrc file

eg at the end of my .bashrc file I write this:

$ cat ~/.bashrc

source /mnt/ngsnfs/globalenv/globalenv

For more details check https://unix.stackexchange.com/questions/26047/how-to-correctly-add-a-path-to-path

The globalenv file should look like this and you can add your bcl2fastq directory in there:

# After changing this remember to source the globalenv again
# After changing environment variables remember to log out and log back in again


########
## Executable files added as directories to PATH
## Keep exactly the same format if you add directories. No blank lines.
########


PATH=/mnt/ngsnfs/tools/gmap/gmap-2016-09-23/bin:\
$JRE_HOME/bin:\
/mnt/ngsnfs/tools/nextflow:\
/mnt/ngsnfs/tools/salmon/build/bin:\
$HOME/bin:$PATH

[yueli7]

Hello, colindaven,

Thank you for your detailed explanation!

Thank you again!

Best,

Yue

Answer 1

[GenoMax]

Your installation seems to be fine. You actually need to have an Illumina flowcell to test the software. 10x makes a small test FC available. It is here. Directions on how to test are under example data section.