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Martin Hope
user977828
Asked: 2022-02-02 16:21:39 +0800 CST
  • 0

我有以下两个文件：

> ls *.ccs.bam
m54105_171201_020331.ccs.bam  m54105_171201_121745.ccs.bam

不幸的是，我未能将它们保存在数组中：

> shopt -s nullglob
> ccs_bams=(*.ccs.bam)
> echo $ccs_bams
m54105_171201_020331.ccs.bam

为什么只打印一个文件？

先感谢您，

bash
Martin Hope
user977828
Asked: 2019-12-28 22:19:33 +0800 CST
  • 10

我可以通过以下方式过滤掉卡在我们的排队系统中的工作：

> qjobs | grep "racon" 
       5240703 racon-3/utg001564l-racon-3.fasta  H   1     1   0     10.0   0.0    150   :03   
       5241418 racon-3/utg002276l-racon-3.fasta  H   1     1   0     10.0   0.0    150   :02   
       5241902 racon-3/utg002759l-racon-3.fasta  H   1     1   0     10.0   0.0    150   :03   
       5242060 racon-3/utg002919l-racon-3.fasta  H   1     1   0     10.0   0.0    150   :04   
       5242273 racon-3/utg003133l-racon-3.fasta  H   1     1   0     10.0   0.0    150   :03   
       5242412 racon-3/utg003270l-racon-3.fasta  H   1     1   0     10.0   0.0    150   :04   
       5242466 racon-3/utg003325l-racon-3.fasta  H   1     1   0     10.0   0.0    150   :03

但是，qjobs | grep "racon" | cut -d " " -f2没有返回例如racon-3/utg003325l-racon-3.fasta。我错过了什么？

grep cut
Martin Hope
user977828
Asked: 2019-12-28 13:54:40 +0800 CST
  • 0

我有很多这些文件，我想知道什么是最高的内存消耗（Mem）

$ cat utg006012l-racon-2.fasta.o5230935
[racon::Polisher::initialize] loaded target sequences 0.013133 s
[racon::Polisher::initialize] loaded sequences 6.667809 s
[racon::Polisher::initialize] loaded overlaps 6.267742 s
[racon::Polisher::initialize] aligning overlaps [=>                  ] 8.633518 s^M[racon::Polisher::initialize] aligning overlaps [==>                 ] 9.058757 s^M[racon::Polisher::initialize] aligning overlaps [===>                ] 9.490215 s^M[racon::Polisher::initialize] aligning overlaps [====>               ] 9.760396 s^M[racon::Polisher::initialize] aligning overlaps [=====>              ] 10.008019 s^M[racon::Polisher::initialize] aligning overlaps [======>             ] 10.332580 s^M[racon::Polisher::initialize] aligning overlaps [=======>            ] 10.681680 s^M[racon::Polisher::initialize] aligning overlaps [========>           ] 11.022209 s^M[racon::Polisher::initialize] aligning overlaps [=========>          ] 11.350026 s^M[racon::Polisher::initialize] aligning overlaps [==========>         ] 11.675731 s^M[racon::Polisher::initialize] aligning overlaps [===========>        ] 12.004713 s^M[racon::Polisher::initialize] aligning overlaps [============>       ] 12.330591 s^M[racon::Polisher::initialize] aligning overlaps [=============>      ] 12.650907 s^M[racon::Polisher::initialize] aligning overlaps [==============>     ] 12.965631 s^M[racon::Polisher::initialize] aligning overlaps [===============>    ] 13.271211 s^M[racon::Polisher::initialize] aligning overlaps [================>   ] 13.553430 s^M[racon::Polisher::initialize] aligning overlaps [=================>  ] 13.825148 s^M[racon::Polisher::initialize] aligning overlaps [==================> ] 14.088558 s^M[racon::Polisher::initialize] aligning overlaps [===================>] 14.350089 s^M[racon::Polisher::initialize] aligning overlaps [====================] 14.598578 s
[racon::Polisher::initialize] transformed data into windows 0.542441 s
[racon::Polisher::polish] generated consensus 11154.363114 s
[racon::Polisher::] total = 11183.003787 s

-----
PBS Job 5230935.pbs
CPU time  : 03:05:52
Wall time : 03:06:38
Mem usage : 4960216kb

我用过grep "Mem" *-racon-2.fasta.o* | cut -d':' -f3 | sed 's|kb||'| sed 's|b||' |awk '{print $1}' | sort，但它没有对输出进行排序

582384
5832
5832
584004
584552
584928
585008
585144
585416
586164
586252
587792
588196
588852
589204
58992
590336
590704
591184
592112
5928
5932
593700
59420
59476
595128
595696
596356
5968
59696
597772
599356
59972
6012
60300
6032
60404
604240
60528
6064
606544
607448
608080

我错过了什么？

先感谢您

awk sed
Martin Hope
user977828
Asked: 2019-08-10 03:28:13 +0800 CST
  • 0

我有以下 Dockerfile：

FROM debian:stretch-backports
RUN apt-get update  && apt-get install -y --no-install-recommends \
        build-essential \
        ruby ruby-dev \
        curl wget \
        gnupg \
        git \
        ncbi-blast+ zlib1g-dev

RUN curl -sL https://deb.nodesource.com/setup_8.x | bash - && \
        apt-get update  && apt-get install -y --no-install-recommends \
        nodejs && \
        rm -rf /var/lib/apt/lists/*

RUN gem install bundler && \
    wget -c https://github.com/wurmlab/sequenceserver/archive/1.1.0.beta12.tar.gz  && \
    tar xfvz 1.1.0.beta12.tar.gz && \
    cd sequenceserver-1.1.0.beta12 && \
    npm install && \
    bundle instal

这导致了以下错误：

...
Installing childprocess 1.0.1 with native extensions
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    current directory: /var/lib/gems/2.3.0/gems/childprocess-1.0.1/ext
/usr/bin/ruby2.3 mkrf_conf.rb

current directory: /var/lib/gems/2.3.0/gems/childprocess-1.0.1/ext
/usr/bin/ruby2.3 -rubygems
/usr/share/rubygems-integration/all/gems/rake-10.5.0/bin/rake
RUBYARCHDIR=/var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/childprocess-1.0.1
RUBYLIBDIR=/var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/childprocess-1.0.1
/usr/bin/ruby2.3: No such file or directory --
/usr/share/rubygems-integration/all/gems/rake-10.5.0/bin/rake (LoadError)

rake failed, exit code 1

Gem files will remain installed in /var/lib/gems/2.3.0/gems/childprocess-1.0.1
for inspection.
Results logged to
/var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/childprocess-1.0.1/gem_make.out

An error occurred while installing childprocess (1.0.1), and Bundler cannot
continue.
Make sure that `gem install childprocess -v '1.0.1' --source
'http://rubygems.org/'` succeeds before bundling.

In Gemfile:
  selenium-webdriver was resolved to 3.142.3, which depends on
    childprocess

我错过了什么？

先感谢您

debian ubuntu
Martin Hope
user977828
Asked: 2019-05-10 17:01:59 +0800 CST
  • 1

我尝试创建一个将文件名存储在文件夹中的数组/列表。以下命令出于未知原因创建了一个:. 怎么可能去掉:？

> a=$(ls split*)
> echo $a
split_sam.o4433568 split_sam.o4433616 split_sam.o4441795 split-data-1:
bash files
Martin Hope
user977828
Asked: 2019-04-15 22:34:09 +0800 CST
  • 0

我有一个包含以下文件内容的文件夹：

ls bams-lab/*.name-sorted.fixmate.sorted.dedup.sam
bams-lab/OZBenth2_.fastp.fq.gz.name-sorted.fixmate.sorted.dedup.sam  
...
bams-lab/OZBenth7_.fastp.fq.gz.name-sorted.fixmate.sorted.dedup.sam

我尝试使用以下 bash 脚本创建文件列表

#!/bin/bash
# usage: sh merge_sam_pbs.sh /path/to/*.name-sorted.fixmate.sorted.dedup.sam 
output=$(dirname $1)
samlist=$(for sam in $1; do echo "I=$sam "; done)
cat << EOF  |cat #qsub
#!/bin/bash -l
#PBS -N merge
#PBS -l walltime=150:00:00
#PBS -j oe
#PBS -l mem=70G
#PBS -l ncpus=2
#PBS -M [email protected]

cd \$PBS_O_WORKDIR

conda activate picard
echo $samlist

picard -Xmx10g  MergeSamFiles \
      $samlist \
      O=${output}/merged.sorted.dedup.bam

EOF

但它只拾取一个文件

> sh merge_sam_pbs.sh bams-lab/*.name-sorted.fixmate.sorted.dedup.sam 
#!/bin/bash -l
#PBS -N merge
#PBS -l walltime=150:00:00
#PBS -j oe
#PBS -l mem=70G
#PBS -l ncpus=2
#PBS -M [email protected]

cd $PBS_O_WORKDIR

conda activate picard
echo I=bams-lab/OZBenth2_.fastp.fq.gz.name-sorted.fixmate.sorted.dedup.sam 

picard -Xmx10g  MergeSamFiles       I=bams-lab/OZBenth2_.fastp.fq.gz.name-sorted.fixmate.sorted.dedup.sam        O=bams-lab/merged.sorted.dedup.bam

我错过了什么？

bash
Martin Hope
user977828
Asked: 2019-03-16 07:25:46 +0800 CST
  • 0

我运行了以下命令

nohup conda activate shuffle_pair_end_reads && python3 shuffle_pair_end_reads.py \
    fastp-filtered-merged4racon/merge_R1.fq.gz \
    fastp-filtered-merged4racon/merge_R2.fq.gz \
    >fastp-filtered-merged4racon/merged_R1_R2.fa \
    2>merged_R1_R2.log &

但不幸的是，我在第二次输入后得到了这个

 nohup: ignoring input and appending output to 'nohup.out'

[1]+  Exit 1                  nohup conda activate shuffle_pair_end_reads && python3 shuffle_pair_end_reads.py fastp-filtered-merged4racon/merge_R1.fq.gz fastp-filtered-merged4racon/merge_R2.fq.gz > fastp-filtered-merged4racon/merged_R1_R2.fa 2> merged_R1_R2.log

我错过了什么？

先感谢您，

bash nohup
Martin Hope
user977828
Asked: 2018-12-29 14:23:05 +0800 CST
  • 0

我未能编译以下软件：

git clone https://github.com/bioinfologics/satsuma2.git
cd satsuma2
cmake
Usage

  cmake [options] <path-to-source>
  cmake [options] <path-to-existing-build>

Specify a source directory to (re-)generate a build system for it in the
current working directory.  Specify an existing build directory to
re-generate its build system.

Run 'cmake --help' for more information.

我错过了什么？

cmake
Martin Hope
user977828
Asked: 2018-10-02 15:15:26 +0800 CST
  • 0

我有一个包含以下内容的文件：

BWA='/software/bwa/bwa-0.7.12/bwa'
SAMTOOLS='/software/samtools/samtools-1.3.1/samtools'

以上工具在我的电脑上：

  • 其中 bwa => /work/waterhouse_team/miniconda2/envs/arima/bin/bwa 和
  • pwd/hic-fq => /scratch/waterhouse_team/benth/dbg2olc-40x/hic-fq

接下来，我使用了这两个sed命令：

sed -i.bak 's|/software/bwa/bwa-0.7.12/bwa|$(which bwa)|g' mapping_arima.sh
sed -i.bak 's|/software/samtools/samtools-1.3.1/samtools|$(which samtools)|g' mapping_arima.sh

不幸的是，作为我收到的输出：

BWA='$(which bwa)'
IN_DIR='$(`pwd`)/hic-fq'

我必须如何更改sed命令才能获得：

  • BWA='/work/waterhouse_team/miniconda2/envs/arima/bin/bwa' 和
  • IN_DIR=/scratch/waterhouse_team/benth/dbg2olc-40x/hic-fq

先感谢您

sed which
Martin Hope
user977828
Asked: 2018-02-02 15:04:27 +0800 CST
  • 0
DASqv -v -H$H -c$cov $db $i | grep Recommend - | sed "s|Recommend ||g" - | sed "s|'||g" -` by itself produces `DAStrim -g20 -b25

我的目标是将之前的结果与awk '{print $1 " " $2 " "$3 " $db $i"}'整个命令结合起来并通过管道输出到一个输出文件> $(basename $i .las).DAStrim。

不幸的是，我只得到结果bananaDB ./bananaDB.100.las，而不是DAStrim -g20 -b25 bananaDB ./bananaDB.100.las以下代码：

#!/bin/bash

db=bananaDB
H=6973
cov=38

for i in $(find . -type f -name "*.*.las");
do
  #cat <<EOF
  qsub <<EOF

#!/bin/bash -l

#PBS -N DASqv
#PBS -l walltime=48:00:00
#PBS -j oe
#PBS -l mem=1G
#PBS -l ncpus=1
#PBS -M [email protected]
##PBS -m bea

cd \$PBS_O_WORKDIR

source activate thegenemyers


DASqv -v -H$H -c$cov $db $i | grep Recommend - | sed "s|Recommend ||g" - | sed "s|'||g" - | awk '{print $1 " " $2 " "$3 " $db $i"}' > $(basename $i .las).DAStrim

EOF

done

更新 

DASqv -v -H$H -c$cov $db $i

制作：

DASqv -c38 bananaDB ./bananaDB.100.las

Input:   16,450reads,   210,758,575 bases (another 9,934 were < H-length)

Histogram of q-values (average 10 best)

                 Input                 QV

    50:    1494189    0.2%       380302   18.0%

    49:     364713    0.0%          484    0.0%
    48:     545846    0.1%          423    0.1%
    47:     650479    0.2%          466    0.1%
    46:     835282    0.3%          548    0.1%
    45:    1054589    0.4%          648    0.1%
    44:    1299423    0.5%          775    0.2%
    43:    1644281    0.7%          895    0.2%
    42:    2036915    0.9%         1193    0.3%
    41:    2571126    1.2%         1334    0.4%
    40:    3518594    1.5%         1647    0.5%
    39:    3641660    1.9%         2046    0.6%
    38:    5026473    2.4%         2291    0.7%
    37:    6243982    3.1%         2708    0.9%
    36:    7600704    3.9%         3301    1.1%
    35:    9313754    4.9%         4002    1.3%
    34:   11257936    6.0%         4676    1.6%
    33:   13508338    7.5%         5544    1.9%
    32:   15981847    9.1%         6552    2.3%
    31:   18648809   11.1%         7771    2.7%
    30:   22290239   13.4%         9124    3.3%
    29:   25083448   16.0%        10624    3.9%
    28:   29566164   19.1%        12874    4.6%
    27:   33339712   22.6%        15482    5.5%
    26:   37891335   26.6%        18869    6.6%
    25:   44146531   31.2%        23307    7.9%
    24:   44948068   35.9%        28142    9.5%
    23:   50951224   41.3%        33590   11.5%
    22:   55009718   47.1%        42157   13.9%
    21:   57456151   53.1%        52181   16.9%
    20:   60635065   59.4%        63207   20.6%
    19:   58423422   65.6%        76426   25.0%
    18:   58472922   71.7%        91565   30.2%
    17:   55127848   77.5%       107289   36.4%
    16:   50395382   82.7%       123758   43.6%
    15:   43893354   87.3%       136465   51.4%
    14:   36509552   91.2%       145632   59.8%
    13:   28654550   94.2%       145540   68.2%
    12:   21245809   96.4%       138232   76.2%
    11:   14560980   97.9%       121403   83.2%
    10:    9345155   98.9%        98071   88.8%
     9:    5395169   99.5%        73996   93.1%
     8:    2894210   99.8%        52246   96.1%
     7:    1335673   99.9%        33845   98.0%
     6:     581470  100.0%        19476   99.2%
     5:     201756  100.0%         9367   99.7%
     4:      76322  100.0%         3760   99.9%
     3:      18979  100.0%         1082  100.0%
     2:       4751  100.0%          264  100.0%
     1:        456  100.0%           41  100.0%
     0:       2686  100.0%           38  100.0%

  Recommend 'DAStrim -g20 -b25'

我错过了什么？

先感谢您。

bash awk