Gaurav Agarwal
Gaurav Agarwal
/usr/local/apps/eb/Roary/3.12.0/bin/query_pan_genome -a gene_multifasta -n fhuE,mog,adaA,group_3839,mgtC,group_14860,trg_11,group_1011,group_1401,atzC,yacG,ushA,group_2341,group_3976,mdoC,ycgZ_1,group_4062,galR,group_1745,lpxH,amiA,group_1714,cynR_2,group_4197,group_1141,fecA,pgrR_3,group_3843,group_842,phoA,uxuA,ispB,dhaM,group_2145,group_2845,fruA_4,srrA,phnM,group_3896,yxeP_1,fhuA_1,atoC_1,inhA,group_2209,ygiC,group_3919,group_2502,motB_2,group_1463,ycfS,gatA_1,group_3819,damX,group_375,group_1702,group_3883,carB,proY,group_1481,lplT,ampC_2,oppF_2,group_2731,yihQ,dlgD,ispH,group_1509,group_2856,entS,group_1057,group_2620,rbsR_1,group_2397,zntB_1,yicJ_3,nagC_6,group_14857,yihS,betT,group_1584,araD,pdeD,atzE,galP,arsC,phoC,por_2,argE_1,btuR,tap_1,ygcS,fimD,group_1405,mrcB,pheC,group_2261,ampH,patB_1,group_3794,pgl_1,pcaK_2,iolS_2,group_3822,lptE,yihP_2,soxS_2,tnaB,znuC,hemH,ribH2,nfrA2,putA,group_2650,group_2367,rebM,soxC,benM_2,pucD,ddpF_2,aspS,group_4068,ydjH,group_14117,pcaF,nuoG,ybjG_2,gldA,rluA_1,hmuU_2,nadK,ttdT,group_784,cyaA,group_2316,group_3825,tsr_4,group_1007,lptC,ghrA_1,trg_8,group_13910,ygiN,moeB_2,xylB_2,pgl_3,group_3972,group_706,group_3835,group_1684,nasA,lpxT,hisI,dhaA,bdlA_1,group_860,yhaJ_1,yisK,ynaI_1,group_598,sbmA,group_1434,group_1505,tus,group_4176,betI_2,lsrR,catD,srlR_2,pstS_1,luxA,group_2490,ascG_2,ydeP_1,amaB,yciV,yihR,dapA_1,budB,dmoA,serS,group_990,group_1537,fhuC_2,msuD,kefF_2,yveA,group_13585,group_3897,group_3795,group_2415,astD,mexB_1,fbaA_5,allS_2,hmuU_1,moaD,virS,kdgK_2,iolS_1,blh,group_2135,group_4180,yjhB_2,group_4178,ddc_2,group_1150,valS,pyrC,mutT,yfgD,xylA_1,yecD,group_2211,gspE,ssuC_2,manR_1,repB,ptrA_1,bmr3,group_2726,group_3834,cirA,group_3950,lgoT_1,iscS,otsA_2,glgB,group_14855,group_3848,dsbD_2,rpoD,tauD,group_283,arsR1,group_1615,arsB,proQ,rpnA_4,group_4072,group_10424,cimH,group_4194,group_3845,cph2,lptG,group_1036,pimB,group_14389,glpK_1,group_4439,group_4038,intA_3,fumD,ssuA_1,cfa,yvbK,group_1909,group_2152,hosA,nimR_2,lolD_2,gatY,group_3840,ecdB,yecN,rraB,dacC,glnH_1,ychF,glnP,ribB,edcC,wecC,group_3918,mngA_1,manP_1,group_2539,group_1594,yycE,cynT,ygiD,nemR_2,bsdD,cex,yqjG,group_4082,mngB,group_2400,group_12999,licR_1,group_3836,otnC,group_509,rutD_1,scrK,group_4084,icsA,group_829,psiF,mug,group_1717,group_1548,group_403,group_4043,group_4314,group_845,lamB_1,group_1134,group_1467,rl5,group_548,group_1635,ble,btr,group_1534,group_3095,auaH,malT,group_2744,atl,rhaA,rhaB,group_1788,cnbH,rppH_1,group_2176,group_2707,group_658,group_4374,yjiG_2,group_698,aaeB_2,group_3941,rhaD,group_3963,tsr_7,group_1626,decR_2,group_986,nicS,rhaM,coaE_2,rhaS_1,leuE,group_2215,group_2391,satP,rhaR,fruA_2,rhaT,group_2291,glpQ *.gff > soft_core_seq.fa
Getting the following error while running scoary. Reading gene presence absence file Traceback (most recent call last): File "/home/ga23981/src/Scoary-master/scoary.py", line 25, in methods.main() File "/home/ga23981/src/Scoary-master/scoary/methods.py", line 215, in main outdir=args.outdir)...
I ran the following perl script perl /apps/eb/Panseq/3.2.1-foss-2019b-Perl-5.30.0/lib/treeNumberToName.pl out/snp.phylip out/phylip_name_conversion.txt > out_tree Gives the following error Could not match 1 Could not match 2 Could not match 3 Could not...
I made multifasta files of genes of interest of several genomes and used them as input files in a directory called genomes as following singularity exec /apps/singularity-images/metachip_1.10.2.sif MetaCHIP PI -p...