[main_samview] fail to read the header
Here is the script for converting the fastq files to Bam files. I keep getting The fail to read the header error. The sam file also comes up empty so I'm not sure what the issue is.
#trimming paired-end
#good version
>&2 echo "Trimming file $base ..."
>&2 date
$javabin/java -jar $trimmomaticbin/$trimmomaticjarfile PE -threads 16 -phred33 $dirname/"$base"_R1_001.fastq.gz $dirname/"$base"_R2_001.fastq.gz $trimdir/"$base"_1.paired.fastq.gz $trimdir/"$base"_1.unpaired.fastq.gz $trimdir/"$base"_2.paired.fastq.gz $trimdir/"$base"_2.unpaired.fastq.gz ILLUMINACLIP:$adapterpath/Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25
>&2 echo "Second stage trimming $base ..."
>&2 date
$kseqbin/kseq_test $trimdir/"$base"_1.paired.fastq.gz $len $trimdir2/"$base"_1.paired.fastq.gz
$kseqbin/kseq_test $trimdir/"$base"_2.paired.fastq.gz $len $trimdir2/"$base"_2.paired.fastq.gz
>&2 echo "Aligning file $base ..."
>&2 date
$bowtie2bin/bowtie2 -p 16 --dovetail --phred33 -x $bt2idx/GRCh38 -1 $trimdir2/"$base"_1.paired.fastq.gz -2 $trimdir2/"$base"_2.paired.fastq.gz > $aligndir/"$base"_aligned_reads.sam 2> $logdir/"$base".bowtie2
$samtoolsbin/samtools view -bS -@ 16 $aligndir/"$base"_aligned_reads.sam > $aligndir/"$base"_aligned_reads.bam
rm $aligndir/"$base"_aligned_reads.sam
>&2 echo "Finished"
>&2 date
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