#typing
head -16000000 R_2017_12_07_15_50_07_user_IONAS-374-DrKobold_PHlab_YK_KELPNO_171207.KLPNC4-trf5504p.IonXpress_017.fastq | gzip -c --best  >  klpn374-4000k.fastq.gz
pwd
cd /data/results/tools/denovo/kmerid/kmerid-master/
time python kmerid.py -f /data/images/proton/external/klpn/plasmid1/klpn374-4000k.fastq.gz  -c config/config.cnf -n
#Kmer based similarities
#similarity	groups	file
94.172722	escherichia	Escherichia_coli_K_12_substr__W3110_uid161931.fa
67.702538	escherichia	Escherichia_coli_W_uid162011.fa
56.832306	escherichia	Escherichia_coli_O157_H7_TW14359_uid59235.fa
54.505398	escherichia	Escherichia_coli_IAI39_uid59381.fa
52.853363	escherichia	Escherichia_coli_SMS_3_5_uid58919.fa
52.828918	escherichia	Escherichia_coli_042_uid161985.fa
50.437317	escherichia	Escherichia_coli_NA114_uid162139.fa
49.821507	escherichia	Escherichia_coli_O127_H6_E2348_69_uid59343.fa
49.435032	escherichia	Escherichia_coli_UM146_uid162043.fa
24.549402	escherichia	Escherichia_fergusonii_ATCC_35469_uid59375.fa
4.362907	salmonella	Salmonella_enterica_serovar_Paratyphi_A_ATCC_9150_uid58201.fa
4.300567	salmonella	Salmonella_enterica_serovar_Javiana_CFSAN001992_uid190101.fa
4.296291	salmonella	Salmonella_enterica_serovar_Gallinarum_pullorum_RKS5078_uid87035.fa
4.220073	salmonella	Salmonella_enterica_serovar_Agona_SL483_uid59431.fa
4.209170	salmonella	Salmonella_enterica_serovar_Choleraesuis_SC_B67_uid58017.fa
4.171369	salmonella	Salmonella_enterica_serovar_Typhi_Ty2_uid57973.fa
4.156878	salmonella	Salmonella_enterica_serovar_Typhimurium_UK_1_uid87049.fa
4.075833	salmonella	Salmonella_enterica_Serovar_Cubana_CFSAN002050_uid212973.fa
3.959964	salmonella	Salmonella_enterica_arizonae_serovar_62_z4_z23__uid58191.fa
3.945707	salmonella	Salmonella_bongori_NCTC_12419_uid70155.fa

# resist.gene test
PATH=/data/results/tools/samtools/samtools-0.1.19:/data/results/tools/align/bowtie2-2.2.8:/data/results/tools/align/tophat-2.1.1.Linux_x86_64:$PATH; export PATH
srst2 --threads 16 --input_se /data/images/proton/external/klpn/plasmid1/R_2017_12_07_15_50_07_user_IONAS-374-DrKobold_PHlab_YK_KELPNO_171207.KLPNC4-trf5504p.IonXpress_017.fastq --output klpn374_test --log --gene_db /data/results/tools/denovo/srst/srst2/data/ARGannot_r2.fasta

# plasmidfinder
srst2 --threads 16 --input_se /data/images/proton/external/klpn/plasmid1/R_2017_12_07_15_50_07_user_IONAS-374-DrKobold_PHlab_YK_KELPNO_171207.KLPNC4-trf5504p.IonXpress_017.fastq --output klpn374_plasmids --log --gene_db /data/results/tools/denovo/srst/srst2/data/PlasmidFinder.fasta

Sample	DB	gene	allele	coverage	depth	diffs	uncertainty	divergence	length	maxMAF	clusterid	seqid	annotation
R_2017_12_07_15_50_07_user_IONAS-374-DrKobold_PHlab_YK_KELPNO_171207.KLPNC4-trf5504p.IonXpress_017	PlasmidFinder	Col	_Col-plasmid_1_J01566__22	98.881	14.295	24snp2indel2holes		9.023	268	0.375	138	_22