Off topic:No bcl2fastq found on path

Question

[yueli7]

Hello,

I tried to use cellranger mkfastq. It said:

No bcl2fastq found on path.

Thanks in advance for great help!

Best,

Yue

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
./usr/local/bin//bcl2fastq
li@li-HP-Pavilion-Desktop-590-p0xxx:~/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin$ echo $PATH
./usr/local/bin/:/home/li/miniconda3/bin:/home/li/.aspera/connect/bin:/home/li/.local/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/snap/bin
li@li-HP-Pavilion-Desktop-590-p0xxx:~/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin$ 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
/home/li/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin
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: 1.18.66.4

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"