#!/bin/sh -f
date_formatted=$(date +%m_%d_%y)
#outputDir=$1
speciesBuild=$1
speciesAbbrev=$2
LOCATION="/illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject"
#move into each directory in location and do
for i in "$LOCATION"/Sample_*; do
#test if i is a file or dir, if so change permissions
test -f "$i" && chmod 755 "$i"
#pass the filename to $infile
infile=`ls $i/*.fastq.gz`
echo "**testing**" $infile
#pass the sample name to $y to append the output directory name
x="$i"
y=${x%.*}
echo ${y}
echo ${y#*/Sample_*}
#count .fastq.gz indexes
#zcat $infile | grep '^@H' | cut -d : -f10 | sort | uniq -c | sort -nr | less > ${y#*/Sample_*}.indices.txt
#run CutAdapt to trim Wafergen adapter
/usr/local/bin/python2.7 /illumina/runs/Runs/cutadapt-1.2.1/bin/cutadapt -a AGATCGGAAGAGCACACGTCT -o $i/${y#*/Sample_*}_cutadapt_AdapterRemoved.fastq.gz $infile
#define cutadapt output as infile2
infile2=`ls $i/*cutadapt_AdapterRemoved.fastq.gz`
echo "**testing**" $infile2
#run QC with FastQC
/illumina/runs/Runs/FastQC/fastqc --outdir=$LOCATION --quiet $infile2
#run sRNAbench w/o adapter trimming
java -jar /illumina/runs/Runs/miRanalyzer/sRNAbenchDB/sRNAbench.jar input=$infile2 output=${y#*/Sample_*}.sRNAbench.$date_formatted dbPath=/illumina/runs/Runs/miRanalyzer/sRNAbenchDB/ species=$speciesBuild microRNA=$speciesAbbrev p=14 noMM=0 alignType=v minRC=2
#move into each fastqc directory in location and send contents of summary.txt to stout
for i in "$LOCATION"/*_fastqc; do
infile3=`ls $i/summary.txt`
echo "***testing***" $infile3
cat <$infile3 >>summary.fastqc.$date_formatted
done
done >stout.miRNA.bash.$date_formatted
The part that is not working is at the end of this code, where I get two outfiles:
summary.fastqc.$date_formatted
Code:
PASS Basic Statistics cutadapt_output_DEHP1_29B.fastq
PASS Per base sequence quality cutadapt_output_DEHP1_29B.fastq
PASS Per sequence quality scores cutadapt_output_DEHP1_29B.fastq
WARN Per base sequence content cutadapt_output_DEHP1_29B.fastq
WARN Per base GC content cutadapt_output_DEHP1_29B.fastq
WARN Per sequence GC content cutadapt_output_DEHP1_29B.fastq
PASS Per base N content cutadapt_output_DEHP1_29B.fastq
FAIL Sequence Length Distribution cutadapt_output_DEHP1_29B.fastq
FAIL Sequence Duplication Levels cutadapt_output_DEHP1_29B.fastq
FAIL Overrepresented sequences cutadapt_output_DEHP1_29B.fastq
FAIL Kmer Content cutadapt_output_DEHP1_29B.fastq
And, stout.miRNA.bash.$date_formatted
Code:
**testing** /illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C/GRC270_DEHP2_67C_CGATGT_L001_R1_001.fastq.gz
/illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C
GRC270_DEHP2_67C
cutadapt version 1.2.1
Command line parameters: -a AGATCGGAAGAGCACACGTCT -o /illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C/GRC270_DEHP2_67C_cutadapt_AdapterRemoved.fastq.gz /illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C/GRC270_DEHP2_67C_CGATGT_L001_R1_001.fastq.gz
Maximum error rate: 10.00%
No. of adapters: 1
Processed reads: 2139267
Processed bases: 109102617 bp (109.1 Mbp)
Trimmed reads: 2075206 (97.0%)
Trimmed bases: 53680380 bp (53.7 Mbp) (49.20% of total)
Too short reads: 0 (0.0% of processed reads)
Too long reads: 0 (0.0% of processed reads)
Total time: 155.78 s
Time per read: 0.07 ms
=== Adapter 1 ===
Adapter 'AGATCGGAAGAGCACACGTCT', length 21, was trimmed 2075206 times.
No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20-21 bp: 2
Lengths of removed sequences
length count expected max. errors
3 13563 33426.0 0
4 13593 8356.5 0
5 19992 2089.1 0
6 143974 522.3 0
7 48435 130.6 0
8 22001 32.6 0
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