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lilab-bcb / cumulus

Cloud-based scalable and efficient single-cell genomics workflows
https://cumulus.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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[error] No bcl2fastq found on path. mkfastq requires bcl2fastq v2.17 or greater for RTA version: 2.4.11 #228

Closed sadiaakter closed 2 years ago

sadiaakter commented 3 years ago

6.0.2: Pulling from cumulusprod/cellranger a330b6cecb98: Pull complete d3b7d82b7494: Pull complete 28ef07914b95: Pull complete 69c7ac712263: Pull complete 50090bb04d6b: Pull complete 95de730468b8: Pull complete 4208f73fd06a: Pull complete 6d6ecf2724e2: Pull complete 2179ee999097: Pull complete 2771ea30cebb: Pull complete Digest: sha256:c92e1071d04461b3d748d3f9f07551f9b7e865a98a24475b7fa9f4a6633dac76 Status: Downloaded newer image for cumulusprod/cellranger:6.0.2 docker.io/cumulusprod/cellranger:6.0.2 /software/cellranger-6.0.2/bin cellranger mkfastq (cellranger-6.0.2) Copyright (c) 2021 10x Genomics, Inc. All rights reserved.

Martian Runtime - v4.0.4 Serving UI at http://compute1-exec-91.ris.wustl.edu:46166?auth=Ex61i3Y0NXJ7UiT9u1qTbJzX1GoGyyqhzH0dgm0Jp7I

Running preflight checks (please wait)...

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

2021-10-14 04:51:20 Shutting down. 2021-10-14 04:51:20 Caught signal terminated 2021-10-14 04:51:20 [monitor] Caught signal terminated Saving pipestance info to "s_200702/s_200702.mri.tgz" For assistance, upload this file to 10x Genomics by running:

cellranger upload "s_200702/s_200702.mri.tgz"

bli25 commented 3 years ago

Hi Sadia,

BCL2FASTQ2 is not open-sourced. Thus, we do not provide it in public dockers. If you want to use this feature, please prepare your own docker and follow instructions here: https://cumulus.readthedocs.io/en/stable/bcl2fastq.html

Best, Bo

Bo Li, Ph.D. Senior Scientist, Data Science and Statistical Computing Genentech, A Member of the Roche Group

On Thu, Oct 14, 2021 at 12:56 AM Sadia Akter @.***> wrote:

6.0.2: Pulling from cumulusprod/cellranger a330b6cecb98: Pull complete d3b7d82b7494: Pull complete 28ef07914b95: Pull complete 69c7ac712263: Pull complete 50090bb04d6b: Pull complete 95de730468b8: Pull complete 4208f73fd06a: Pull complete 6d6ecf2724e2: Pull complete 2179ee999097: Pull complete 2771ea30cebb: Pull complete Digest: sha256:c92e1071d04461b3d748d3f9f07551f9b7e865a98a24475b7fa9f4a6633dac76 Status: Downloaded newer image for cumulusprod/cellranger:6.0.2 docker.io/cumulusprod/cellranger:6.0.2 /software/cellranger-6.0.2/bin cellranger mkfastq (cellranger-6.0.2) Copyright (c) 2021 10x Genomics, Inc. All rights reserved.

Martian Runtime - v4.0.4 Serving UI at http://compute1-exec-91.ris.wustl.edu:46166?auth=Ex61i3Y0NXJ7UiT9u1qTbJzX1GoGyyqhzH0dgm0Jp7I

Running preflight checks (please wait)...

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

2021-10-14 04:51:20 Shutting down. 2021-10-14 04:51:20 Caught signal terminated 2021-10-14 04:51:20 [monitor] Caught signal terminated Saving pipestance info to "s_200702/s_200702.mri.tgz" For assistance, upload this file to 10x Genomics by running:

cellranger upload "s_200702/s_200702.mri.tgz"

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