Tenho os dois arquivos a seguir:
> ls *.ccs.bam
m54105_171201_020331.ccs.bam m54105_171201_121745.ccs.bam
Infelizmente, não consigo protegê-los na matriz:
> shopt -s nullglob
> ccs_bams=(*.ccs.bam)
> echo $ccs_bams
m54105_171201_020331.ccs.bam
Por que apenas um arquivo é impresso?
Agradeço antecipadamente,
Em nosso ambiente de nuvem, peguei o Debian e agora gostaria de instalar um desktop. Qual área de trabalho suporta um ícone de atualização para notificar sobre atualizações.
Eu sou capaz de filtrar os trabalhos que ficaram presos em nosso sistema de filas com:
> 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
No entanto, qjobs | grep "racon" | cut -d " " -f2não retornou, por exemplo racon-3/utg003325l-racon-3.fasta. O que eu perdi?
Tenho muitos desses arquivos e gostaria de saber qual é o maior consumo de memória (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
Eu usei grep "Mem" *-racon-2.fasta.o* | cut -d':' -f3 | sed 's|kb||'| sed 's|b||' |awk '{print $1}' | sort, mas não classificou a saída
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
O que eu perdi?
Agradeço antecipadamente
Eu tenho o seguinte 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
que causou o seguinte erro:
...
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
O que eu perdi?
Agradeço antecipadamente
Eu tento criar uma matriz/lista que armazena nomes de arquivos dentro de uma pasta. O comando abaixo cria por motivos desconhecidos um arquivo :. Como é possível remover :?
> a=$(ls split*)
> echo $a
split_sam.o4433568 split_sam.o4433616 split_sam.o4441795 split-data-1:
Eu tenho uma pasta com o seguinte conteúdo de arquivo:
ls bams-lab/*.name-sorted.fixmate.sorted.dedup.sam
bams-lab/OZBenth2_.fastp.fq.gz.name-sorted.fixmate.sorted.dedup.sam
...
bams-lab/OZBenth7_.fastp.fq.gz.name-sorted.fixmate.sorted.dedup.sam
Eu tentei criar uma lista de arquivos com o script bash abaixo
#!/bin/bash
# usage: sh merge_sam_pbs.sh /path/to/*.name-sorted.fixmate.sorted.dedup.sam
output=$(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
mas só pega um arquivo
> 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 $PBS_O_WORKDIR
conda activate picard
echo I=bams-lab/OZBenth2_.fastp.fq.gz.name-sorted.fixmate.sorted.dedup.sam
picard -Xmx10g MergeSamFiles I=bams-lab/OZBenth2_.fastp.fq.gz.name-sorted.fixmate.sorted.dedup.sam O=bams-lab/merged.sorted.dedup.bam
O que eu perdi?
rodei o seguinte comando
nohup conda activate shuffle_pair_end_reads && python3 shuffle_pair_end_reads.py \
fastp-filtered-merged4racon/merge_R1.fq.gz \
fastp-filtered-merged4racon/merge_R2.fq.gz \
>fastp-filtered-merged4racon/merged_R1_R2.fa \
2>merged_R1_R2.log &
mas infelizmente, consegui isso depois de pressionar a segunda vez enter
nohup: ignoring input and appending output to 'nohup.out'
[1]+ Exit 1 nohup conda activate shuffle_pair_end_reads && python3 shuffle_pair_end_reads.py fastp-filtered-merged4racon/merge_R1.fq.gz fastp-filtered-merged4racon/merge_R2.fq.gz > fastp-filtered-merged4racon/merged_R1_R2.fa 2> merged_R1_R2.log
O que eu perdi?
Agradeço antecipadamente,
usei o comando abaixo
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz > fastp-filtered-merged4racon/merge_R1.fq.gz > merge_R1.out.log 2>&1 &
mas infelizmente, a saída foi para merge_R1.out.loge não para merge_R1.fq.gz.
O que eu perdi?
Não consegui compilar o software abaixo:
git clone https://github.com/bioinfologics/satsuma2.git
cd satsuma2
cmake
Usage
cmake [options] <path-to-source>
cmake [options] <path-to-existing-build>
Specify a source directory to (re-)generate a build system for it in the
current working directory. Specify an existing build directory to
re-generate its build system.
Run 'cmake --help' for more information.
O que eu perdi?
Tenho um arquivo com o seguinte conteúdo:
BWA='/software/bwa/bwa-0.7.12/bwa'
SAMTOOLS='/software/samtools/samtools-1.3.1/samtools'
As ferramentas acima estão no meu computador:
pwd/hic-fq => /scratch/waterhouse_team/benth/dbg2olc-40x/hic-fqEm seguida, usei esses dois sedcomandos:
sed -i.bak 's|/software/bwa/bwa-0.7.12/bwa|$(which bwa)|g' mapping_arima.sh
sed -i.bak 's|/software/samtools/samtools-1.3.1/samtools|$(which samtools)|g' mapping_arima.sh
Infelizmente, como saída, recebi:
BWA='$(which bwa)'
IN_DIR='$(`pwd`)/hic-fq'
Como eu tenho que alterar os sedcomandos para obter:
Agradeço antecipadamente
DASqv -v -H$H -c$cov $db $i | grep Recommend - | sed "s|Recommend ||g" - | sed "s|'||g" -` by itself produces `DAStrim -g20 -b25
Meu objetivo é combinar os resultados anteriores awk '{print $1 " " $2 " "$3 " $db $i"}'e canalizar todo o comando para um arquivo de saída > $(basename $i .las).DAStrim.
Infelizmente, só obtenho como resultado bananaDB ./bananaDB.100.lase não DAStrim -g20 -b25 bananaDB ./bananaDB.100.lascom o seguinte código:
#!/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 $i .las).DAStrim
EOF
done
ATUALIZAR
DASqv -v -H$H -c$cov $db $i
produzido:
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'
O que eu perdi?
Agradeço antecipadamente.