+ PROJECT=PRJNA313294
+ GTF=/home/www/refs/Homo_sapiens.GRCh38.96.chr.gtf
+ RUNINFO=runinfo.all.csv
+ SINGLE=runinfo.single.csv
+ PAIRED=runinfo.paired.csv
+ READNUM=1000000
+ REF=/home/www/refs/Homo_sapiens.GRCh38.cdna.all.fa
+ IDX=/home/www/refs/Homo_sapiens.GRCh38.cdna.all.idx
+ esearch -db sra -query PRJNA313294
+ efetch -format runinfo
+ cat runinfo.all.csv
+ cut -f 1 -d ,
+ grep 'SRR.*SINGLE'
+ cat runinfo.all.csv
+ cut -f 1 -d ,
+ grep 'SRR.*PAIRED'
+ cat runinfo.single.csv
+ parallel fastq-dump -X 1000000 -O reads
+ cat runinfo.paired.csv
+ parallel fastq-dump -X 1000000 --split-files -O reads
+ kallisto index -i /home/www/refs/Homo_sapiens.GRCh38.cdna.all.idx /home/www/refs/Homo_sapiens.GRCh38.cdna.all.fa

[build] loading fasta file /home/www/refs/Homo_sapiens.GRCh38.cdna.all.fa
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
        from 1431 target sequences
[build] warning: replaced 5 non-ACGUT characters in the input sequence
        with pseudorandom nucleotides
[build] counting k-mers ... done.
[build] building target de Bruijn graph ...  done 
[build] creating equivalence classes ...  done
[build] target de Bruijn graph has 1131887 contigs and contains 109544288 k-mers 

+ mkdir -p results
+ cat runinfo.single.csv
+ parallel kallisto quant -i /home/www/refs/Homo_sapiens.GRCh38.cdna.all.idx -o 'results/{}' --single -l 187 -s 70 'reads/{}.fastq'
+ cat runinfo.paired.csv
+ parallel kallisto quant -i /home/www/refs/Homo_sapiens.GRCh38.cdna.all.idx -o 'results/{}' -l 187 -s 70 'reads/{}_1.fastq' 'reads/{}_2.fastq'
+ cat runinfo.single.csv runinfo.paired.csv
+ parallel 'cut -f 1,4 results/{}/abundance.tsv > results/{}.txt'
+ paste results/SRR3191542.txt results/SRR3191543.txt results/SRR3194428.txt results/SRR3194429.txt
+ cut -f 1,2,4,6,8
+ paste results/SRR3191544.txt results/SRR3191545.txt results/SRR3194430.txt results/SRR3194431.txt
+ cut -f 1,2,4,6,8
+ paste mock.txt zikv.txt
+ cut -f 1-5,7-11
+ cat counts.txt
+ awk ' ($2+$3+$4+$5+$6+$7+$8+$9) > 25 { print $0 } '
+ cat over25.txt
+ awk ' { printf("%s\t%4.0f\t%4.0f\t%4.0f\t%4.0f\t%4.0f\t%4.0f\t%4.0f\t%4.0f\n", $1, $2, $3, $4, $5, $6, $7, $8, $9) } '
+ wget -q -nc http://data.biostarhandbook.com/rnaseq/code/deseq1.r
+ cat valid.txt
+ Rscript deseq1.r 4x4
+ wget -q -nc http://data.biostarhandbook.com/rnaseq/code/draw-heatmap.r
+ cat norm-matrix-deseq1.txt
+ Rscript draw-heatmap.r