/data/results/tools/align/bowtie2-2.2.3/bowtie2 -x bb_wo_ins IonXpress_015_IMP3_Ab42Round2.fq  --un unpaired.bam --al unaligned.bam > /dev/null
13825029 reads; of these:
  13825029 (100.00%) were unpaired; of these:
    3318079 (24.00%) aligned 0 times
    10506950 (76.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
76.00% overall alignment rate

/data/results/tools/align/bowtie2-2.2.3/bowtie2 -x bb_wo_ins IonXpress_011_IMP2_A4VRound4.fq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > IonXpress_011_IMP2_A4VRound4.aligned.bam

15233125 reads; of these:
  15233125 (100.00%) were unpaired; of these:
    7881760 (51.74%) aligned 0 times
    7351365 (48.26%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
48.26% overall alignment rate
/data/results/tools/align/bowtie2-2.2.3/bowtie2 -x bb_wo_ins IonXpress_011_IMP2_A4VRound4.fq   --al IMP2-unaligned.bam > /dev/null


/data/results/tools/align/bowtie2-2.2.3/bowtie2 -x bb_wo_ins IonXpress_009_IMP1_4-5-6-7PeptideLinrary.fq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > IonXpress_009_IMP1_4-5-6-7PeptideLinrary.aligned.bam


16102381 reads; of these:
  16102381 (100.00%) were unpaired; of these:
    7311491 (45.41%) aligned 0 times
    8790890 (54.59%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
54.59% overall alignment rate

/data/results/tools/align/bowtie2-2.2.3/bowtie2 -p 8 -x bb_wo_ins IonXpress_009_IMP1_4-5-6-7PeptideLinrary.fq   --al IMP1-unaligned.bam > /dev/null

awk -f /data/results/tools/formats/fastq2fasta.awk unaligned.bam | head -2000 | /data/results/tools/align/blast/ncbi-blast-2.2.29+/bin/blastx -db /data/results/reference/ncbi/nr  -num_threads 6 -max_target_seqs 1 -outfmt='6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen staxids sscinames scomnames' > IMP3-unmapped-blast1000.txt

awk -f /data/results/tools/formats/fastq2fasta.awk IMP1-unaligned.bam | head -2000 | /data/results/tools/align/blast/ncbi-blast-2.2.29+/bin/blastx -db /data/results/reference/ncbi/nr  -num_threads 8 -max_target_seqs 1 -outfmt='6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen staxids sscinames scomnames' > IMP1-unmapped-blast1000.txt


/data/results/tools/align/bowtie2-2.2.3/bowtie2 -p 8 -x bb_wo_ins IonXpress_011_IMP2_A4VRound4.fq   --al IMP2-unaligned.bam > /dev/null
awk -f /data/results/tools/formats/fastq2fasta.awk IMP2-unaligned.bam | head -2000 | /data/results/tools/align/blast/ncbi-blast-2.2.29+/bin/blastx -db /data/results/reference/ncbi/nr  -num_threads 8 -max_target_seqs 1 -outfmt='6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen staxids sscinames scomnames' > IMP2-unmapped-blast1000.txt

awk -f /data/results/tools/formats/blast2species-stats1.awk IMP1-unmapped-blast1000.txt  > IMP1-unmapped-blast1000-species.txt
awk -f /data/results/tools/formats/blast2species-stats1.awk IMP2-unmapped-blast1000.txt  > IMP2-unmapped-blast1000-species.txt
awk -f /data/results/tools/formats/blast2species-stats1.awk IMP3-unmapped-blast1000.txt  > IMP3-unmapped-blast1000-species.txt