Question: bcl2fastq on Mac
0
gravatar for New2R
4 months ago by
New2R20
New2R20 wrote:

Does bcl2fastq work on a mac? bcl2fastq is available as a Linux rpm file bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm. I tried extracting the the rpm contents by first installing rpm2cpio on mac using brew

brew install rpm2cpio

seen here (http://macappstore.org/rpm2cpio/). Then extracted contents using

rpm2cpio.pl bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm | cpio -idmv

This extracts the contents with the binary located with the following folder path usr/local/bin/bcl2fastq. I tried executing the bcl2fastq using command

/usr/local/bin/bcl2fastq --runfolder-dir <RunFolder> --output-dir <BaseCalls>

But this did not work. It errors out saying that the binary is not executable. I tried chmod +x. But not successful.

Anybody successfully able to run this on mac. Or is this a Linux distribution with no hope on a mac. Appreciate any help with this.

next-gen • 482 views
ADD COMMENTlink modified 9 weeks ago by GokalpC40 • written 4 months ago by New2R20
1

You can always try conda

ADD REPLYlink written 4 months ago by RamRS21k

Or..... the old school way - run Linux inside a VM

ADD REPLYlink written 4 months ago by Santosh Anand4.8k

Please, no. There is no upside to using a Linux VM on a Mac, especially given that running custom Linux binaries of any flavor is virtually invisible unless one is working on the shell.

EDIT: For some software, you'll have to take the VM route. Looks like bcl2fastq is one of those software applications where VM is the only way to go.

ADD REPLYlink modified 4 months ago • written 4 months ago by RamRS21k

I tried conda and installed bcl2fastq-nextseq. Now I am having trouble executing it. I tried

 bcl_to_fastq 
-R /path to runfolder-dir/ 
-O /path to output-dir/ 
--ignore-missing

It gave me the following error

Using /Users/path to runfolder-dir/SampleSheet.csv
[2019-02-07 10:32:08 - INFO] Processing /path to runfolder-dir/SampleSheet.csv
[2019-02-07 10:32:08 - INFO] Found 55 samples for run 190111_NB501338_0413_AHFFWMAFXY
[2019-02-07 10:32:08 - INFO] Run complete.
[2019-02-07 10:32:08 - INFO] Converting .bcl to .fastq using: $>bcl2fastq -r 12 -d 12 -p 24 -w 12 --barcode-mismatches 0 --no-lane-splitting -R . -R /path to runfolder-dir/ -O /path to output-dir --ignore-missing
Traceback (most recent call last):
  File "/Users/sampaths/anaconda2/bin/bcl_to_fastq", line 11, in <module>
    load_entry_point('bcl2fastq==1.2.4', 'console_scripts', 'bcl_to_fastq')()
  File "/Users/sampaths/anaconda2/lib/python2.7/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/Users/sampaths/anaconda2/lib/python2.7/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/Users/sampaths/anaconda2/lib/python2.7/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/sampaths/anaconda2/lib/python2.7/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/Users/sampaths/anaconda2/lib/python2.7/site-packages/bcl2fastq.py", line 319, in bcl2fastq
    call_status = run_bcl2fastq(runfolder, cmd_args)
  File "/Users/sampaths/anaconda2/lib/python2.7/site-packages/bcl2fastq.py", line 143, in run_bcl2fastq
    sp.check_call(cmd, stdout=fh, stderr=fh, shell=True)
  File "/Users/sampaths/anaconda2/lib/python2.7/subprocess.py", line 190, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'bcl2fastq -r 12 -d 12 -p 24 -w 12 --barcode-mismatches 0 --no-lane-splitting -R . -R /path to runfolder-dir/ -O /path to output-dir --ignore-missing' returned non-zero exit status 127

I contacted the author at GitHub and he told me that there extenal dependancies not available at bioconda. The Illumina documentation here https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2_guide_15051736_v2.pdf (page 26) indicates zlib, librt and libpthread as dependancies.

zib was present in anaconda, but there other two were not available. The bcl2fastq.log file had this written to file

/bin/sh: bcl2fastq: command not found
/bin/sh: bcl2fastq: command not found

So I am not sure how I should proceed from here.

ADD REPLYlink written 4 months ago by New2R20

I'm guessing bcl2fastq was not built to play well with macOS. You're better off taking the VM route as advised by Santosh Anand.

ADD REPLYlink written 4 months ago by RamRS21k
0
gravatar for GokalpC
9 weeks ago by
GokalpC40
Turkey/Ankara/Intergen
GokalpC40 wrote:

Why don't you try docker for mac.

You can try various images under docker hub.

I recently released a compatible build with many kernel versions.

docker pull skysbiodocker/bcl2fastq2
ADD COMMENTlink written 9 weeks ago by GokalpC40
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