Question: (Closed) No bcl2fastq found on path
gravatar for yueli7
3 months ago by
yueli7140 wrote:


I tried to use cellranger mkfastq. It said:

No bcl2fastq found on path.

Thanks in advance for great help!



li@li-HP-Pavilion-Desktop-590-p0xxx:~/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin$ bcl2fastq --version
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.

li@li-HP-Pavilion-Desktop-590-p0xxx:~/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin$ which bcl2fastq
li@li-HP-Pavilion-Desktop-590-p0xxx:~/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin$ echo $PATH
li@li-HP-Pavilion-Desktop-590-p0xxx:~/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin$ export PATH=$PATH:/use/local/bin
li@li-HP-Pavilion-Desktop-590-p0xxx:~/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin$ ./cellranger mkfastq --id=tiny-bcl  --run=cellranger-tiny-bcl-1.2.0  --csv=cellranger-tiny-bcl-simple-1.2.0.csv
cellranger mkfastq (3.1.0)
      Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.

Martian Runtime - '3.1.0-v3.2.3'
2020-02-11 00:55:48 [jobmngr] WARNING: configured to use 21GB of local memory, but only 20.7GB is currently available.
2020-02-11 00:55:48 [runtime] Reattaching in local mode.
Serving UI at http://li-HP-Pavilion-Desktop-590-p0xxx:46879?auth=p5vOshipcC_GSyF15yfkCdSGpzTZKHxzr9a3zrBxZlw

2020-02-11 00:55:48 [runtime] (reset-partial)   ID.tiny-bcl.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT.fork0.chnk0
2020-02-11 00:55:48 [runtime] (reset-partial)   ID.tiny-bcl.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT_LOCAL.fork0.chnk0
2020-02-11 00:55:48 [runtime] Found orphaned local stage: ID.tiny-bcl.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT_LOCAL
2020-02-11 00:55:48 [runtime] Found orphaned local stage: ID.tiny-bcl.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT

[error] No bcl2fastq found on path. demux requires bcl2fastq v2.17 or greater for RTA version:

2020-02-11 00:55:48 Shutting down.
Waiting 6 seconds for UI to do final refresh.
2020-02-11 00:55:48 Caught signal terminated
2020-02-11 00:55:48 [monitor] Caught signal terminated
Saving pipestance info to "tiny-bcl/tiny-bcl.mri.tgz"
For assistance, upload this file to 10x Genomics by running:

cellranger upload <your_email> "tiny-bcl/tiny-bcl.mri.tgz"
rna-seq bcl2fastq • 188 views
ADD COMMENTlink modified 3 months ago by zx87549.2k • written 3 months ago by yueli7140

I guess you need to install bcl2fastq...

ADD REPLYlink written 3 months ago by gb1.8k

Hello yueli7!

We believe that this post does not fit the main topic of this site.

Install bcl2fastq and ann to PATH

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink written 3 months ago by ATpoint35k

You asked this before: install bcl2fastq

If you are so stuck with the basics then please try to find any kind of Unix system administrator at your institution that guides you.

ADD REPLYlink written 3 months ago by ATpoint35k
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