我一直在按照官网教程安装cellranger的过程,前面都没什么问题。到了mkfastq这一步的时候用了官网给的测试数据运行测试,就出了这个问题。
说是bcl2fastq在运行过程中被打断了。但是软件也没有给出具体的原因。
[root@DESKTOP-QGBSIH6 admin]# cellranger mkfastq --id=tutorial --run=/mnt/g/cellranger/mkfastq/cellranger-tiny-bcl-1.2.0 --csv=/mnt/g/cellranger/mkfastq/cellranger-tiny-bcl-simple-1.2.0.csv
/mnt/g/cellranger/cellranger-7.0.1/bin
cellranger mkfastq (cellranger-7.0.1)
Copyright (c) 2021 10x Genomics, Inc. All rights reserved.
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Martian Runtime - v4.0.8
2022-11-16 21:44:28 [runtime] Reattaching in local mode.
Serving UI at http://DESKTOP-QGBSIH6:61881?auth=r8EtzVfKTuenr_zyyq0vaiRYJcBZRV27D3wNGe1UG70
2022-11-16 21:44:28 [runtime] (reset-partial) ID.tutorial.MAKE_FASTQS_CS.MAKE_FASTQS.BCL2FASTQ_WITH_SAMPLESHEET.fork0.chnk0
2022-11-16 21:44:28 [runtime] Found orphaned local stage: ID.tutorial.MAKE_FASTQS_CS.MAKE_FASTQS.BCL2FASTQ_WITH_SAMPLESHEET
2022-11-16 21:44:28 [runtime] (split_complete) ID.tutorial.MAKE_FASTQS_CS.MAKE_FASTQS.BCL2FASTQ_WITH_SAMPLESHEET
2022-11-16 21:44:28 [runtime] (run:local) ID.tutorial.MAKE_FASTQS_CS.MAKE_FASTQS.BCL2FASTQ_WITH_SAMPLESHEET.fork0.chnk0.main
2022-11-16 21:44:29 [runtime] (failed) ID.tutorial.MAKE_FASTQS_CS.MAKE_FASTQS.BCL2FASTQ_WITH_SAMPLESHEET
[error] bcl2fastq was killed with signal -11.
2022-11-16 21:44:29 Shutting down.
Saving pipestance info to "tutorial/tutorial.mri.tgz"
For assistance, upload this file to 10x Genomics by running:
cellranger upload "tutorial/tutorial.mri.tgz"
用的是在服务器上面安装的虚拟机centos7,cellranger用的是7.0.1版本的。bcl2fastq用的是2.20版本的。数据操作什么的都是跟官网一样的,只是路径不同。
在各个网站删都搜索过这个结果了,但是没有相关的问题。甚至还给cellranger官方发了邮件,不过感觉没有什么回复。
能够正常运行cellranger就行。本来老板只要求我跑一个数据。
你把教程发给我,我看一下有没有错误的步骤