search

domenico-simone / tutorials

:books: Various bioinformatics tutorials
https://hadrieng.github.io/tutorials/
Other
0 stars 2 forks source link

Whole Metagenome sequencing (https://www.hadriengourle.com/tutorials/wms/) #2

Open FahmidazamanIrin opened 4 years ago

FahmidazamanIrin commented 4 years ago

I have followed instructions and command but Kraken did not work. Here is the command I have used and the error message I got:

(base) [fahmi@rackham3 uppmax_tutorial]$ cd Whole_Metagenome_Sequencing/ (base) [fahmi@rackham3 Whole_Metagenome_Sequencing]$ ll total 4 drwxrwsr-x 5 fahmi g2020005 4096 Feb 18 11:38 wms (base) [fahmi@rackham3 Whole_Metagenome_Sequencing]$ cd wms/ (base) [fahmi@rackham3 wms]$ ll total 12 drwxrwsr-x 3 fahmi g2020005 4096 Feb 18 11:39 data drwxrwsr-x 2 fahmi g2020005 4096 Feb 18 12:33 results drwxrwsr-x 2 fahmi g2020005 4096 Feb 18 11:38 scripts (base) [fahmi@rackham3 wms]$ cd results/ (base) [fahmi@rackham3 results]$ ll total 0 -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR1135369.tab -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR1135369_tax.txt -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR1135370.tab -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR1135370_tax.txt -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR1135375.tab -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR1135375_tax.txt -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR321573.tab -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR321573_tax.txt -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR321574.tab -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR321574_tax.txt -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR321578.tab -rw-rw-r-- 1 fahmi g2020005 0 Feb 18 21:55 ERR321578_tax.txt (base) [fahmi@rackham3 results]$ cd .. (base) [fahmi@rackham3 wms]$ cd data/ (base) [fahmi@rackham3 data]$ ll total 108468 drwxrwsr-x 3 fahmi g2020005 4096 Feb 18 12:20 sub_100000 -rw-rw-r-- 1 fahmi g2020005 111061046 Feb 18 11:39 subset_wms.tar.gz (base) [fahmi@rackham3 data]$ cd sub_100000/ (base) [fahmi@rackham3 sub_100000]$ ll total 377468 -rw-rw-r-- 1 fahmi g2020005 33150182 Feb 13 2018 ERR1135369_1.fastq -rw-rw-r-- 1 fahmi g2020005 228955 Feb 18 12:00 ERR1135369_1_fastqc.html -rw-rw-r-- 1 fahmi g2020005 257152 Feb 18 11:59 ERR1135369_1_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 32938080 Feb 13 2018 ERR1135369_2.fastq -rw-rw-r-- 1 fahmi g2020005 229772 Feb 18 12:01 ERR1135369_2_fastqc.html -rw-rw-r-- 1 fahmi g2020005 259564 Feb 18 12:01 ERR1135369_2_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 33122456 Feb 13 2018 ERR1135370_1.fastq -rw-rw-r-- 1 fahmi g2020005 235448 Feb 18 12:02 ERR1135370_1_fastqc.html -rw-rw-r-- 1 fahmi g2020005 301203 Feb 18 12:02 ERR1135370_1_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 32984558 Feb 13 2018 ERR1135370_2.fastq -rw-rw-r-- 1 fahmi g2020005 233807 Feb 18 12:03 ERR1135370_2_fastqc.html -rw-rw-r-- 1 fahmi g2020005 294788 Feb 18 12:03 ERR1135370_2_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 33219722 Feb 13 2018 ERR1135375_1.fastq -rw-rw-r-- 1 fahmi g2020005 231171 Feb 18 12:04 ERR1135375_1_fastqc.html -rw-rw-r-- 1 fahmi g2020005 259417 Feb 18 12:03 ERR1135375_1_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 33023644 Feb 13 2018 ERR1135375_2.fastq -rw-rw-r-- 1 fahmi g2020005 229816 Feb 18 12:04 ERR1135375_2_fastqc.html -rw-rw-r-- 1 fahmi g2020005 259657 Feb 18 12:04 ERR1135375_2_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 30356728 Feb 13 2018 ERR321573_1.fastq -rw-rw-r-- 1 fahmi g2020005 231078 Feb 18 12:05 ERR321573_1_fastqc.html -rw-rw-r-- 1 fahmi g2020005 252036 Feb 18 12:05 ERR321573_1_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 30357090 Feb 13 2018 ERR321573_2.fastq -rw-rw-r-- 1 fahmi g2020005 229326 Feb 18 12:05 ERR321573_2_fastqc.html -rw-rw-r-- 1 fahmi g2020005 249725 Feb 18 12:05 ERR321573_2_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 30357716 Feb 13 2018 ERR321574_1.fastq -rw-rw-r-- 1 fahmi g2020005 226578 Feb 18 12:06 ERR321574_1_fastqc.html -rw-rw-r-- 1 fahmi g2020005 244735 Feb 18 12:06 ERR321574_1_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 30358332 Feb 13 2018 ERR321574_2.fastq -rw-rw-r-- 1 fahmi g2020005 225567 Feb 18 12:06 ERR321574_2_fastqc.html -rw-rw-r-- 1 fahmi g2020005 248333 Feb 18 12:06 ERR321574_2_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 30346800 Feb 13 2018 ERR321578_1.fastq -rw-rw-r-- 1 fahmi g2020005 227466 Feb 18 12:06 ERR321578_1_fastqc.html -rw-rw-r-- 1 fahmi g2020005 246338 Feb 18 12:06 ERR321578_1_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 30347300 Feb 13 2018 ERR321578_2.fastq -rw-rw-r-- 1 fahmi g2020005 228823 Feb 18 12:06 ERR321578_2_fastqc.html -rw-rw-r-- 1 fahmi g2020005 253850 Feb 18 12:06 ERR321578_2_fastqc.zip -rw-rw-r-- 1 fahmi g2020005 119 Feb 13 2018 metadata.txt drwxrwsr-x 3 fahmi g2020005 4096 Feb 18 12:21 mnt (base) [fahmi@rackham3 sub_100000]$ cd mnt/ (base) [fahmi@rackham3 mnt]$ ll total 4 drwxrwsr-x 3 fahmi g2020005 4096 Feb 18 12:22 databases (base) [fahmi@rackham3 mnt]$ cd databases/ (base) [fahmi@rackham3 databases]$ ll total 2879488 drwxrwsr-x 3 fahmi g2020005 4096 Oct 20 2017 minikraken_20171013_4GB -rw-rw-r-- 1 fahmi g2020005 2948586452 Oct 20 2017 minikraken_20171019_4GB.tgz (base) [fahmi@rackham3 databases]$ for i in *_1.fastq

do prefix=$(basename $i _1.fastq) echo $prefix kraken --db $KRAKEN_DB --threads 2 --fastq-input \ ${prefix}_1.fastq ${prefix}_2.fastq /proj/g2020005/nobackup/fahmi/uppmax_tutorial/Whole_Metagenome_Sequencing/wms/results/${prefix}.tab kraken-report --db $KRAKEN_DB \ /proj/g2020005/nobackup/fahmi/uppmax_tutorial/Whole_Metagenome_Sequencing/wms/results/${prefix}.tab /proj/g2020005/nobackup/fahmi/uppmax_tutorial/Whole_Metagenome_Sequencing/wms/results/${prefix}_tax.txt done minikraken_20171013_4GB minikraken_20171019_4GB.tgz -bash: kraken: command not found -bash: /proj/g2020005/nobackup/fahmi/uppmax_tutorial/Whole_Metagenome_Sequencing/wms/results/ERR1135369.tab: Permission denied -bash: kraken-report: command not found -bash: /proj/g2020005/nobackup/fahmi/uppmax_tutorial/Whole_Metagenome_Sequencing/wms/results/ERR1135369_tax.txt: Permission denied