/data/results/tools/align/bowtie2-2.3.2/bowtie2 -x /data/images/proton/run149/bb_wo_ins R_2020_10_09_13_06_35_user_IONAS-454-EMQN2_DrSkr-Bagr_VAlab_201009_EMQNb_GSkP_VA16s_TB3R.GSkP7_A.IonXpress_031.fastq | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > GSkP7_A.bam /data/results/tools/align/bowtie2-2.3.2/bowtie2 -x /data/images/proton/run149/bb_wo_ins R_2020_10_09_13_06_35_user_IONAS-454-EMQN2_DrSkr-Bagr_VAlab_201009_EMQNb_GSkP_VA16s_TB3R.GSkP8_b.IonXpress_032.fastq | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > GSkP8_b.bam #/data/results/tools/align/bowtie2-2.2.3/bowtie2 -x /data/images/proton/run149/bb_wo_ins R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSkP4-Ab42Lib.IonXpressRNA_015.fq | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSkP4-Ab42Lib.IonXpressRNA_015.bam /data/results/tools/align/bowtie2-2.2.8/bowtie2 -x /data/images/proton/run149/bb_wo_ins ../R_2016_04_19_11_40_37_user_IONAS-288-ITlab-PHlab-DrSkretas_160419_ITC109_PHR16-17_GSKP4-5.GSKP4-Ab42.IonXpress_015.fastq | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > R_2016_04_19_11_40_37_user_IONAS-288-ITlab-PHlab-DrSkretas_160419_ITC109_PHR16-17_GSKP4-5.GSKP4-Ab42.IonXpress_015.fastq.bam 3813591 reads; of these: 3813591 (100.00%) were unpaired; of these: 1708736 (44.81%) aligned 0 times 2104855 (55.19%) aligned exactly 1 time 0 (0.00%) aligned >1 times 55.19% overall alignment rate /data/results/tools/align/bowtie2-2.2.8/bowtie2 -x /data/images/proton/run149/bb_wo_ins ../R_2016_04_19_11_40_37_user_IONAS-288-ITlab-PHlab-DrSkretas_160419_ITC109_PHR16-17_GSKP4-5.GSKP5-SOD.IonXpress_016.fastq | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > R_2016_04_19_11_40_37_user_IONAS-288-ITlab-PHlab-DrSkretas_160419_ITC109_PHR16-17_GSKP4-5.GSKP5-SOD.IonXpress_016.fastq.bam 7852313 reads; of these: 7852313 (100.00%) were unpaired; of these: 894022 (11.39%) aligned 0 times 6958291 (88.61%) aligned exactly 1 time 0 (0.00%) aligned >1 times 88.61% overall alignment rate #reczko@max:/data/results/tools/align/jvarkit/samtools-htsjdk-96aa8be$ ant htsjdk-jar export JAVA_HOME=/home/reczko/a/tools/libs/java/jdk1.8.0_66 apt-get install xsltproc reczko@max:/data/results/tools/align/jvarkit/jvarkit-master$ make biostar59647 /mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/dist/biostar59647 ln -s /data/images/proton/run149/backbone_wo_insert.dict ln -s /data/images/proton/run149/backbone_wo_insert.fa ln -s /data/images/proton/run149/backbone_wo_insert.fa.fai #test #samtools view R_2016_04_19_11_40_37_user_IONAS-288-ITlab-PHlab-DrSkretas_160419_ITC109_PHR16-17_GSKP4-5.GSKP4-Ab42.IonXpress_015.fastq.bam | head -9999 >foo #cat backbone_wo_insert.dict foo| java -Djvarkit.log.name=biostar59647 -Dfile.encoding=UTF8 -Xmx500m -cp "/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/htsjdk-8dd4559dced3a243dde094415a9974c03aceb3e3/dist/apache-ant-1.8.2-bzip2.jar:/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/htsjdk-8dd4559dced3a243dde094415a9974c03aceb3e3/dist/commons-compress-1.4.1.jar:/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/htsjdk-8dd4559dced3a243dde094415a9974c03aceb3e3/dist/commons-jexl-2.1.1.jar:/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/htsjdk-8dd4559dced3a243dde094415a9974c03aceb3e3/dist/commons-logging-1.1.1.jar:/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/htsjdk-8dd4559dced3a243dde094415a9974c03aceb3e3/dist/htsjdk-2.1.1.jar:/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/htsjdk-8dd4559dced3a243dde094415a9974c03aceb3e3/dist/ngs-java-1.2.2.jar:/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/htsjdk-8dd4559dced3a243dde094415a9974c03aceb3e3/dist/snappy-java-1.0.3-rc3.jar:/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/htsjdk-8dd4559dced3a243dde094415a9974c03aceb3e3/dist/xz-1.5.jar:/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/lib/commons-cli/commons-cli/1.3.1/commons-cli-1.3.1.jar:/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/lib/org/slf4j/slf4j-api/1.7.13/slf4j-api-1.7.13.jar:/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/lib/org/slf4j/slf4j-simple/1.7.13/slf4j-simple-1.7.13.jar:/mnt/fix/b/solid.data_results.recovered.data/tools/align/jvarkit/jvarkit-master/dist/biostar59647.jar" com.github.lindenb.jvarkit.tools.biostar.Biostar59647 -r backbone_wo_insert.fa foo ref:9-20 | xmllint --format - |awk -f /data/images/proton/run149/extract_insert1.awk > foo.fa samtools view R_2016_04_19_11_40_37_user_IONAS-288-ITlab-PHlab-DrSkretas_160419_ITC109_PHR16-17_GSKP4-5.GSKP4-Ab42.IonXpress_015.fastq.bam | split -199999 ./get-ins2.sh for i in *ins do cat $i >> ins.fa done for i in *ins do cat $i >> ins.fa done mv ins.fa GSKP4-Ab42.IonXpress_015.fa /data/results/tools/align/multiple/cd-hit-v4.6.1-2012-08-27/cd-hit-est -i GSKP4-Ab42.IonXpress_015.fa -o GSKP4-Ab42.IonXpress_015.fa.clust -c 0.95 -n 5 -S 0 -r 0 -M 40000 &> GSKP4-Ab42.IonXpress_015.fa.log echo "GSKP4-Ab42.IonXpress_015.fa.clust" | awk -f /data/results/tools/align/multiple/cd-hit-clust-sizes1.awk samtools view R_2016_04_19_11_40_37_user_IONAS-288-ITlab-PHlab-DrSkretas_160419_ITC109_PHR16-17_GSKP4-5.GSKP5-SOD.IonXpress_016.fastq.bam | split -199999 ./get-ins2.sh /data/results/tools/align/multiple/cd-hit-v4.6.1-2012-08-27/cd-hit-est -i GSKP5-SOD.IonXpress_016.fa -o GSKP5-SOD.IonXpress_016.fa.clust -c 0.95 -n 5 -S 0 -r 0 -M 40000 &> GSKP5-SOD.IonXpress_016.fa.log echo "GSKP5-SOD.IonXpress_016.fa.clust" | awk -f /data/results/tools/align/multiple/cd-hit-clust-sizes1.awk ls *.clstr.size.fa > insert_samples.txt awk -f merge-inserts3.awk insert_samples.txt > insert_samples.csv