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软件没有发现在路径上

发表于 : 2020-02-12 10:37
yueli711
各位大侠,

我已经在/home/li下面安装了bcl2fastq, 怎么运行的时候就

代码: 全选

No bcl2fastq found on path
先谢谢了!

代码: 全选

[email protected]:~$ bcl2fastq --help
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.

Usage:
  bcl2fastq [options]






[email protected]:~$ 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 20:16:39 [jobmngr] WARNING: configured to use 21GB of local memory, but only 19.0GB is currently available.
2020-02-11 20:16:39 [runtime] Reattaching in local mode.
Serving UI at http://li-HP-Pavilion-Desktop-590-p0xxx:39889?auth=ECJkP0tXgwBHrQwqlcZBN1UtFck0Of4F83ahq6jb0OU

2020-02-11 20:16:39 [runtime] (reset-partial)   ID.tiny-bcl.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT.fork0.chnk0
2020-02-11 20:16:39 [runtime] (reset-partial)   ID.tiny-bcl.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT_LOCAL.fork0.chnk0
2020-02-11 20:16:39 [runtime] Found orphaned local stage: ID.tiny-bcl.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT
2020-02-11 20:16:39 [runtime] Found orphaned local stage: ID.tiny-bcl.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT_LOCAL

[error] No bcl2fastq found on path. demux requires bcl2fastq v2.17 or greater for RTA version: 1.18.66.4

Re: 软件没有发现在路径上

发表于 : 2020-02-12 12:04
astolia
官方叫你发邮件到技术支持去 https://github.com/10XGenomics/cellranger/issues/6

Re: 软件没有发现在路径上

发表于 : 2020-02-13 2:18
yueli711
Hello, astolia,

那个邮件昨天晚上已经发了。 还是这里高人多。

先谢谢了!

yue

[email protected]:~$ export PATH="/usr/local/bin:$PATH"
[email protected]:~$ bcl2fastq --h
bcl2fastq: command not found

[email protected]:~$ export PATH="./usr/local/bin:$PATH"
[email protected]:~$ bcl2fastq --h
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.

Usage:
bcl2fastq [options]



[email protected]:~$ which bcl2fastq
./usr/local/bin/bcl2fastq

Re: 软件没有发现在路径上

发表于 : 2020-02-13 3:18
astolia
谁教你的往PATH里放相对路径的?

Re: 软件没有发现在路径上

发表于 : 2020-02-13 3:53
yueli711
astolia, 您好!

感谢回复!

这个链接 https://kb.10xgenomics.com/hc/en-us/art ... bcl2fastq-

[email protected]:~$ which bcl2fastq
​​./usr/local/bin/bcl2fastq

Re: 软件没有发现在路径上

发表于 : 2020-02-13 11:45
astolia
yueli711 写了:
2020-02-13 3:53
astolia, 您好!

感谢回复!

这个链接 https://kb.10xgenomics.com/hc/en-us/art ... bcl2fastq-

[email protected]:~$ which bcl2fastq
​​./usr/local/bin/bcl2fastq
这个链接里哪里提到了PATH环境变量?净自作聪明