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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Issue with bcl2fastq #6

Closed sbhattacharya3 closed 6 years ago

sbhattacharya3 commented 6 years ago

Hi,

I have installed bcl2fastq and cell ranger, for using the mkfastq command. It was working fine, but it has just stopped working. To verify whether I messed up with the PATH, I installed cell ranger and bcl2fastq on a different system, and run the commands from there. I am still getting errors. Please find below the commands

Checking the version of bcl2fastq

[sbhattach2@CRI-13-130 cellranger-2.1.0]$ bcl2fastq --version BCL to FASTQ file converter bcl2fastq v2.20.0.422 Copyright (c) 2007-2017 Illumina, Inc.

running mkfastq

[sbhattach2@CRI-13-130 cellranger-2.1.0]$ sudo ./cellranger mkfastq --id=single_cell_zhe --run=/data/Suro/180112_NS500434_0271_AHFCW5BGX5/ --samplesheet=/home/sbhattach2/Sample_Zhe.csv /home/sbhattach2/cellranger-2.1.0/cellranger-cs/2.1.0/bin cellranger mkfastq (2.1.0) Copyright (c) 2017 10x Genomics, Inc. All rights reserved.

Martian Runtime - '2.1.0-2.3.0' Serving UI at http://CRI-13-130:34100?auth=HvO_950umeofy7Jo1aYtXyKrK3lEiBUDzbXi_pjVOZ0

Running preflight checks (please wait)... Checking run folder... Checking RunInfo.xml... Checking system environment... Checking barcode whitelist... Checking read specification... Checking samplesheet specs...

[error] No bcl2fastq found on path. demux requires bcl2fastq v2.17 or greater for RTA version: 2.4.11

Can you please guide me regarding the changes I need to make?

Thanks in advance, Surajit

pryvkin10x commented 6 years ago

Hello,

I assume you were able to get help through our official support email since this question relates to an official release.