========================================================== Starting on : Thu Jul 18 18:16:51 EDT 2019 Running on node : scc-ka3 Current directory : /restricted/projectnb/waxmanlab/varsha/cufflinks Current job ID : 7805251 Current job name : mergeCuffAll Task index number : ========================================================== /scratch/7805251.1.linga Running on host scc-ka3 Directory is /scratch/7805251.1.linga Start time is Thu Jul 18 18:16:51 EDT 2019 Tisha_lncRNAs /restricted/projectnb/waxmanlab/varsha/cufflinks/Tisha/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Tisha/transcripts.gtf Tisha_lncRNAs.gtf PAPL1 /restricted/projectnb/waxmanlab/varsha/cufflinks/APAPL1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/APAPL1_cufflinks/transcripts.gtf PAPL1.gtf APAPL2 /restricted/projectnb/waxmanlab/varsha/cufflinks/APAPL2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/APAPL2_cufflinks/transcripts.gtf APAPL2.gtf APAPL3 /restricted/projectnb/waxmanlab/varsha/cufflinks/APAPL3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/APAPL3_cufflinks/transcripts.gtf APAPL3.gtf LRH-APAPL1 /restricted/projectnb/waxmanlab/varsha/cufflinks/LRH-APAPL1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/LRH-APAPL1_cufflinks/transcripts.gtf LRH-APAPL1.gtf LRH-APAPL2 /restricted/projectnb/waxmanlab/varsha/cufflinks/LRH-APAPL2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/LRH-APAPL2_cufflinks/transcripts.gtf LRH-APAPL2.gtf VL1 /restricted/projectnb/waxmanlab/varsha/cufflinks/VL1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/VL1_cufflinks/transcripts.gtf VL1.gtf VL2 /restricted/projectnb/waxmanlab/varsha/cufflinks/VL2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/VL2_cufflinks/transcripts.gtf VL2.gtf VL3 /restricted/projectnb/waxmanlab/varsha/cufflinks/VL3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/VL3_cufflinks/transcripts.gtf VL3.gtf IC57-1 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1_cufflinks/transcripts.gtf IC57-1.gtf IC57-2 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-2_cufflinks/transcripts.gtf IC57-2.gtf IC57-3 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-3_cufflinks/transcripts.gtf IC57-3.gtf IC57-4 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-4_cufflinks/transcripts.gtf IC57-4.gtf IC57-6 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-6_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-6_cufflinks/transcripts.gtf IC57-6.gtf IC57-7 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-7_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-7_cufflinks/transcripts.gtf IC57-7.gtf IC57-8 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-8_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-8_cufflinks/transcripts.gtf IC57-8.gtf IC57-9 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-9_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-9_cufflinks/transcripts.gtf IC57-9.gtf IC57-1149 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1149_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1149_cufflinks/transcripts.gtf IC57-1149.gtf IC57-1150 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1150_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1150_cufflinks/transcripts.gtf IC57-1150.gtf IC57-1151 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1151_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1151_cufflinks/transcripts.gtf IC57-1151.gtf IC57-1152 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1152_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1152_cufflinks/transcripts.gtf IC57-1152.gtf IC57-1159 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1159_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1159_cufflinks/transcripts.gtf IC57-1159.gtf IC57-1160 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1160_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1160_cufflinks/transcripts.gtf IC57-1160.gtf IC57-1161 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1161_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1161_cufflinks/transcripts.gtf IC57-1161.gtf IC57-1162 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1162_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1162_cufflinks/transcripts.gtf IC57-1162.gtf IC57-1164 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1164_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1164_cufflinks/transcripts.gtf IC57-1164.gtf IC57-1165 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1165_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1165_cufflinks/transcripts.gtf IC57-1165.gtf IC57-1166 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1166_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1166_cufflinks/transcripts.gtf IC57-1166.gtf IC57-1167 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1167_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1167_cufflinks/transcripts.gtf IC57-1167.gtf IC57-1169 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1169_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1169_cufflinks/transcripts.gtf IC57-1169.gtf IC57-1170 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1170_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1170_cufflinks/transcripts.gtf IC57-1170.gtf IC57-1171 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1171_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1171_cufflinks/transcripts.gtf IC57-1171.gtf IC57-1172 /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1172_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IC57-1172_cufflinks/transcripts.gtf IC57-1172.gtf I-R-1 /restricted/projectnb/waxmanlab/varsha/cufflinks/I-R-1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/I-R-1_cufflinks/transcripts.gtf I-R-1.gtf I-R-2 /restricted/projectnb/waxmanlab/varsha/cufflinks/I-R-2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/I-R-2_cufflinks/transcripts.gtf I-R-2.gtf I-R-3 /restricted/projectnb/waxmanlab/varsha/cufflinks/I-R-3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/I-R-3_cufflinks/transcripts.gtf I-R-3.gtf IPO-1 /restricted/projectnb/waxmanlab/varsha/cufflinks/IPO-1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IPO-1_cufflinks/transcripts.gtf IPO-1.gtf IPO-2 /restricted/projectnb/waxmanlab/varsha/cufflinks/IPO-2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IPO-2_cufflinks/transcripts.gtf IPO-2.gtf IPO-3 /restricted/projectnb/waxmanlab/varsha/cufflinks/IPO-3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/IPO-3_cufflinks/transcripts.gtf IPO-3.gtf N-1 /restricted/projectnb/waxmanlab/varsha/cufflinks/N-1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/N-1_cufflinks/transcripts.gtf N-1.gtf N-2 /restricted/projectnb/waxmanlab/varsha/cufflinks/N-2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/N-2_cufflinks/transcripts.gtf N-2.gtf N-3 /restricted/projectnb/waxmanlab/varsha/cufflinks/N-3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/N-3_cufflinks/transcripts.gtf N-3.gtf 1h_MitoCDNB_1 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_1_cufflinks/transcripts.gtf 1h_MitoCDNB_1.gtf 1h_MitoCDNB_2 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_2_cufflinks/transcripts.gtf 1h_MitoCDNB_2.gtf 1h_MitoCDNB_3 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_3_cufflinks/transcripts.gtf 1h_MitoCDNB_3.gtf 1h_MitoCDNB_4 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_4_cufflinks/transcripts.gtf 1h_MitoCDNB_4.gtf 1h_MitoCDNB_5 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_5_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_5_cufflinks/transcripts.gtf 1h_MitoCDNB_5.gtf 1h_MitoCDNB_6 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_6_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_MitoCDNB_6_cufflinks/transcripts.gtf 1h_MitoCDNB_6.gtf 1h_Vehicle_1 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_1_cufflinks/transcripts.gtf 1h_Vehicle_1.gtf 1h_Vehicle_2 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_2_cufflinks/transcripts.gtf 1h_Vehicle_2.gtf 1h_Vehicle_3 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_3_cufflinks/transcripts.gtf 1h_Vehicle_3.gtf 1h_Vehicle_4 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_4_cufflinks/transcripts.gtf 1h_Vehicle_4.gtf 1h_Vehicle_5 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_5_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_5_cufflinks/transcripts.gtf 1h_Vehicle_5.gtf 1h_Vehicle_6 /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_6_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1h_Vehicle_6_cufflinks/transcripts.gtf 1h_Vehicle_6.gtf 4h_MitoCDNB_1 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_1_cufflinks/transcripts.gtf 4h_MitoCDNB_1.gtf 4h_MitoCDNB_2 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_2_cufflinks/transcripts.gtf 4h_MitoCDNB_2.gtf 4h_MitoCDNB_3 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_3_cufflinks/transcripts.gtf 4h_MitoCDNB_3.gtf 4h_MitoCDNB_4 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_4_cufflinks/transcripts.gtf 4h_MitoCDNB_4.gtf 4h_MitoCDNB_5 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_5_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_5_cufflinks/transcripts.gtf 4h_MitoCDNB_5.gtf 4h_MitoCDNB_6 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_6_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_MitoCDNB_6_cufflinks/transcripts.gtf 4h_MitoCDNB_6.gtf 4h_Vehicle_1 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_1_cufflinks/transcripts.gtf 4h_Vehicle_1.gtf 4h_Vehicle_2 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_2_cufflinks/transcripts.gtf 4h_Vehicle_2.gtf 4h_Vehicle_3 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_3_cufflinks/transcripts.gtf 4h_Vehicle_3.gtf 4h_Vehicle_4 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_4_cufflinks/transcripts.gtf 4h_Vehicle_4.gtf 4h_Vehicle_5 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_5_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_5_cufflinks/transcripts.gtf 4h_Vehicle_5.gtf 4h_Vehicle_6 /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_6_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4h_Vehicle_6_cufflinks/transcripts.gtf 4h_Vehicle_6.gtf 1_Liver_Basal_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_Basal_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_Basal_20_cufflinks/transcripts.gtf 1_Liver_Basal_20.gtf 1_Liver_Low_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_Low_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_Low_20_cufflinks/transcripts.gtf 1_Liver_Low_20.gtf 1_Liver_High_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_High_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_High_20_cufflinks/transcripts.gtf 1_Liver_High_20.gtf 1_Liver_Basal_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_Basal_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_Basal_3h_cufflinks/transcripts.gtf 1_Liver_Basal_3h.gtf 1_Liver_Low_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_Low_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_Low_3h_cufflinks/transcripts.gtf 1_Liver_Low_3h.gtf 1_Liver_High_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_High_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/1_Liver_High_3h_cufflinks/transcripts.gtf 1_Liver_High_3h.gtf 2_Liver_Basal_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_Basal_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_Basal_20_cufflinks/transcripts.gtf 2_Liver_Basal_20.gtf 2_Liver_Low_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_Low_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_Low_20_cufflinks/transcripts.gtf 2_Liver_Low_20.gtf 2_Liver_High_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_High_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_High_20_cufflinks/transcripts.gtf 2_Liver_High_20.gtf 2_Liver_Basal_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_Basal_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_Basal_3h_cufflinks/transcripts.gtf 2_Liver_Basal_3h.gtf 2_Liver_Low_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_Low_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_Low_3h_cufflinks/transcripts.gtf 2_Liver_Low_3h.gtf 2_Liver_High_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_High_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/2_Liver_High_3h_cufflinks/transcripts.gtf 2_Liver_High_3h.gtf 3_Liver_Basal_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_Basal_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_Basal_20_cufflinks/transcripts.gtf 3_Liver_Basal_20.gtf 3_Liver_Low_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_Low_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_Low_20_cufflinks/transcripts.gtf 3_Liver_Low_20.gtf 3_Liver_High_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_High_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_High_20_cufflinks/transcripts.gtf 3_Liver_High_20.gtf 3_Liver_Basal_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_Basal_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_Basal_3h_cufflinks/transcripts.gtf 3_Liver_Basal_3h.gtf 3_Liver_Low_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_Low_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_Low_3h_cufflinks/transcripts.gtf 3_Liver_Low_3h.gtf 3_Liver_High_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_High_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/3_Liver_High_3h_cufflinks/transcripts.gtf 3_Liver_High_3h.gtf 4_Liver_Basal_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_Basal_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_Basal_20_cufflinks/transcripts.gtf 4_Liver_Basal_20.gtf 4_Liver_Low_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_Low_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_Low_20_cufflinks/transcripts.gtf 4_Liver_Low_20.gtf 4_Liver_High_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_High_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_High_20_cufflinks/transcripts.gtf 4_Liver_High_20.gtf 4_Liver_Basal_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_Basal_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_Basal_3h_cufflinks/transcripts.gtf 4_Liver_Basal_3h.gtf 4_Liver_Low_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_Low_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_Low_3h_cufflinks/transcripts.gtf 4_Liver_Low_3h.gtf 4_Liver_High_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_High_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/4_Liver_High_3h_cufflinks/transcripts.gtf 4_Liver_High_3h.gtf 5_Liver_Basal_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/5_Liver_Basal_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/5_Liver_Basal_20_cufflinks/transcripts.gtf 5_Liver_Basal_20.gtf 5_Liver_Low_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/5_Liver_Low_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/5_Liver_Low_20_cufflinks/transcripts.gtf 5_Liver_Low_20.gtf 5_Liver_High_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/5_Liver_High_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/5_Liver_High_20_cufflinks/transcripts.gtf 5_Liver_High_20.gtf 5_Liver_Basal_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/5_Liver_Basal_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/5_Liver_Basal_3h_cufflinks/transcripts.gtf 5_Liver_Basal_3h.gtf 6_Liver_Basal_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_Basal_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_Basal_20_cufflinks/transcripts.gtf 6_Liver_Basal_20.gtf 6_Liver_Low_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_Low_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_Low_20_cufflinks/transcripts.gtf 6_Liver_Low_20.gtf 6_Liver_High_20 /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_High_20_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_High_20_cufflinks/transcripts.gtf 6_Liver_High_20.gtf 6_Liver_Basal_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_Basal_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_Basal_3h_cufflinks/transcripts.gtf 6_Liver_Basal_3h.gtf 6_Liver_Low_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_Low_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_Low_3h_cufflinks/transcripts.gtf 6_Liver_Low_3h.gtf 6_Liver_High_3h /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_High_3h_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/6_Liver_High_3h_cufflinks/transcripts.gtf 6_Liver_High_3h.gtf Old-Cntrl-HTV1 /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-Cntrl-HTV1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-Cntrl-HTV1_cufflinks/transcripts.gtf Old-Cntrl-HTV1.gtf Old-Cntrl-HTV2 /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-Cntrl-HTV2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-Cntrl-HTV2_cufflinks/transcripts.gtf Old-Cntrl-HTV2.gtf Old-Cntrl-HTV3 /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-Cntrl-HTV3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-Cntrl-HTV3_cufflinks/transcripts.gtf Old-Cntrl-HTV3.gtf Old-Cntrl-HTV4 /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-Cntrl-HTV4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-Cntrl-HTV4_cufflinks/transcripts.gtf Old-Cntrl-HTV4.gtf Old-hMANF-HTV1 /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-hMANF-HTV1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-hMANF-HTV1_cufflinks/transcripts.gtf Old-hMANF-HTV1.gtf Old-hMANF-HTV2 /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-hMANF-HTV2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-hMANF-HTV2_cufflinks/transcripts.gtf Old-hMANF-HTV2.gtf Old-hMANF-HTV3 /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-hMANF-HTV3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-hMANF-HTV3_cufflinks/transcripts.gtf Old-hMANF-HTV3.gtf Old-hMANF-HTV4 /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-hMANF-HTV4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Old-hMANF-HTV4_cufflinks/transcripts.gtf Old-hMANF-HTV4.gtf Yg-Cntrl-HTV2 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-Cntrl-HTV2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-Cntrl-HTV2_cufflinks/transcripts.gtf Yg-Cntrl-HTV2.gtf Yg-Cntrl-HTV4 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-Cntrl-HTV4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-Cntrl-HTV4_cufflinks/transcripts.gtf Yg-Cntrl-HTV4.gtf Yg-hMANF-HTV1 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-hMANF-HTV1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-hMANF-HTV1_cufflinks/transcripts.gtf Yg-hMANF-HTV1.gtf Yg-hMANF-HTV2 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-hMANF-HTV2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-hMANF-HTV2_cufflinks/transcripts.gtf Yg-hMANF-HTV2.gtf Yg-hMANF-HTV3 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-hMANF-HTV3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-hMANF-HTV3_cufflinks/transcripts.gtf Yg-hMANF-HTV3.gtf Yg-hMANF-HTV4 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-hMANF-HTV4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg-hMANF-HTV4_cufflinks/transcripts.gtf Yg-hMANF-HTV4.gtf O-O1 /restricted/projectnb/waxmanlab/varsha/cufflinks/O-O1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O-O1_cufflinks/transcripts.gtf O-O1.gtf O-O2 /restricted/projectnb/waxmanlab/varsha/cufflinks/O-O2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O-O2_cufflinks/transcripts.gtf O-O2.gtf O-O3 /restricted/projectnb/waxmanlab/varsha/cufflinks/O-O3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O-O3_cufflinks/transcripts.gtf O-O3.gtf O-O4 /restricted/projectnb/waxmanlab/varsha/cufflinks/O-O4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O-O4_cufflinks/transcripts.gtf O-O4.gtf O-O5 /restricted/projectnb/waxmanlab/varsha/cufflinks/O-O5_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O-O5_cufflinks/transcripts.gtf O-O5.gtf O_YgHet_1 /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgHet_1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgHet_1_cufflinks/transcripts.gtf O_YgHet_1.gtf O_YgHet_2 /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgHet_2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgHet_2_cufflinks/transcripts.gtf O_YgHet_2.gtf O_YgHet_3 /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgHet_3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgHet_3_cufflinks/transcripts.gtf O_YgHet_3.gtf O_YgHet_4 /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgHet_4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgHet_4_cufflinks/transcripts.gtf O_YgHet_4.gtf O_YgHet_5 /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgHet_5_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgHet_5_cufflinks/transcripts.gtf O_YgHet_5.gtf O_YgWT_1 /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgWT_1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgWT_1_cufflinks/transcripts.gtf O_YgWT_1.gtf O_YgWT_2 /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgWT_2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgWT_2_cufflinks/transcripts.gtf O_YgWT_2.gtf O_YgWT_3 /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgWT_3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgWT_3_cufflinks/transcripts.gtf O_YgWT_3.gtf O_YgWT_4 /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgWT_4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgWT_4_cufflinks/transcripts.gtf O_YgWT_4.gtf O_YgWT_5 /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgWT_5_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/O_YgWT_5_cufflinks/transcripts.gtf O_YgWT_5.gtf Yg_Het1 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_Het1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_Het1_cufflinks/transcripts.gtf Yg_Het1.gtf Yg_Het2 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_Het2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_Het2_cufflinks/transcripts.gtf Yg_Het2.gtf Yg_Het3 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_Het3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_Het3_cufflinks/transcripts.gtf Yg_Het3.gtf Yg_Het4 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_Het4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_Het4_cufflinks/transcripts.gtf Yg_Het4.gtf Yg_Het5 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_Het5_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_Het5_cufflinks/transcripts.gtf Yg_Het5.gtf Yg_WT1 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_WT1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_WT1_cufflinks/transcripts.gtf Yg_WT1.gtf Yg_WT2 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_WT2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_WT2_cufflinks/transcripts.gtf Yg_WT2.gtf Yg_WT3 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_WT3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_WT3_cufflinks/transcripts.gtf Yg_WT3.gtf Yg_WT4 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_WT4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_WT4_cufflinks/transcripts.gtf Yg_WT4.gtf Yg_WT5 /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_WT5_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Yg_WT5_cufflinks/transcripts.gtf Yg_WT5.gtf GFP_1347 /restricted/projectnb/waxmanlab/varsha/cufflinks/GFP_1347_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/GFP_1347_cufflinks/transcripts.gtf GFP_1347.gtf GFP_1369 /restricted/projectnb/waxmanlab/varsha/cufflinks/GFP_1369_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/GFP_1369_cufflinks/transcripts.gtf GFP_1369.gtf GFP_1371 /restricted/projectnb/waxmanlab/varsha/cufflinks/GFP_1371_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/GFP_1371_cufflinks/transcripts.gtf GFP_1371.gtf Nudt7_1357 /restricted/projectnb/waxmanlab/varsha/cufflinks/Nudt7_1357_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Nudt7_1357_cufflinks/transcripts.gtf Nudt7_1357.gtf Nudt7_1359 /restricted/projectnb/waxmanlab/varsha/cufflinks/Nudt7_1359_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Nudt7_1359_cufflinks/transcripts.gtf Nudt7_1359.gtf Nudt7_1365 /restricted/projectnb/waxmanlab/varsha/cufflinks/Nudt7_1365_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Nudt7_1365_cufflinks/transcripts.gtf Nudt7_1365.gtf Nudt7_2305 /restricted/projectnb/waxmanlab/varsha/cufflinks/Nudt7_2305_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/Nudt7_2305_cufflinks/transcripts.gtf Nudt7_2305.gtf CHOW1 /restricted/projectnb/waxmanlab/varsha/cufflinks/CHOW1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/CHOW1_cufflinks/transcripts.gtf CHOW1.gtf CHOW2 /restricted/projectnb/waxmanlab/varsha/cufflinks/CHOW2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/CHOW2_cufflinks/transcripts.gtf CHOW2.gtf CHOW3 /restricted/projectnb/waxmanlab/varsha/cufflinks/CHOW3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/CHOW3_cufflinks/transcripts.gtf CHOW3.gtf NASH_OA-NO2_1 /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA-NO2_1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA-NO2_1_cufflinks/transcripts.gtf NASH_OA-NO2_1.gtf NASH_OA-NO2_2 /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA-NO2_2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA-NO2_2_cufflinks/transcripts.gtf NASH_OA-NO2_2.gtf NASH_OA-NO2_3 /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA-NO2_3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA-NO2_3_cufflinks/transcripts.gtf NASH_OA-NO2_3.gtf NASH_OA1 /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA1_cufflinks/transcripts.gtf NASH_OA1.gtf NASH_OA2 /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA2_cufflinks/transcripts.gtf NASH_OA2.gtf NASH_OA3 /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_OA3_cufflinks/transcripts.gtf NASH_OA3.gtf NASH_PEG1 /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_PEG1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_PEG1_cufflinks/transcripts.gtf NASH_PEG1.gtf NASH_PEG2 /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_PEG2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_PEG2_cufflinks/transcripts.gtf NASH_PEG2.gtf NASH_PEG3 /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_PEG3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/NASH_PEG3_cufflinks/transcripts.gtf NASH_PEG3.gtf WT_1 /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_1_cufflinks/transcripts.gtf WT_1.gtf WT_2 /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_2_cufflinks/transcripts.gtf WT_2.gtf WT_3 /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_3_cufflinks/transcripts.gtf WT_3.gtf WT_4 /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_4_cufflinks/transcripts.gtf WT_4.gtf MANFHet_1 /restricted/projectnb/waxmanlab/varsha/cufflinks/MANFHet_1_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/MANFHet_1_cufflinks/transcripts.gtf MANFHet_1.gtf MANFHet_2 /restricted/projectnb/waxmanlab/varsha/cufflinks/MANFHet_2_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/MANFHet_2_cufflinks/transcripts.gtf MANFHet_2.gtf MANFHet_3 /restricted/projectnb/waxmanlab/varsha/cufflinks/MANFHet_3_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/MANFHet_3_cufflinks/transcripts.gtf MANFHet_3.gtf MANFHet_4 /restricted/projectnb/waxmanlab/varsha/cufflinks/MANFHet_4_cufflinks/transcripts.gtf cp /restricted/projectnb/waxmanlab/varsha/cufflinks/MANFHet_4_cufflinks/transcripts.gtf MANFHet_4.gtf cp .gtf cp: missing destination file operand after '.gtf' Try 'cp --help' for more information. Tisha_lncRNAs.gtf PAPL1.gtf APAPL2.gtf APAPL3.gtf LRH-APAPL1.gtf LRH-APAPL2.gtf VL1.gtf VL2.gtf VL3.gtf IC57-1.gtf IC57-2.gtf IC57-3.gtf IC57-4.gtf IC57-6.gtf IC57-7.gtf IC57-8.gtf IC57-9.gtf IC57-1149.gtf IC57-1150.gtf IC57-1151.gtf IC57-1152.gtf IC57-1159.gtf IC57-1160.gtf IC57-1161.gtf IC57-1162.gtf IC57-1164.gtf IC57-1165.gtf IC57-1166.gtf IC57-1167.gtf IC57-1169.gtf IC57-1170.gtf IC57-1171.gtf IC57-1172.gtf I-R-1.gtf I-R-2.gtf I-R-3.gtf IPO-1.gtf IPO-2.gtf IPO-3.gtf N-1.gtf N-2.gtf N-3.gtf 1h_MitoCDNB_1.gtf 1h_MitoCDNB_2.gtf 1h_MitoCDNB_3.gtf 1h_MitoCDNB_4.gtf 1h_MitoCDNB_5.gtf 1h_MitoCDNB_6.gtf 1h_Vehicle_1.gtf 1h_Vehicle_2.gtf 1h_Vehicle_3.gtf 1h_Vehicle_4.gtf 1h_Vehicle_5.gtf 1h_Vehicle_6.gtf 4h_MitoCDNB_1.gtf 4h_MitoCDNB_2.gtf 4h_MitoCDNB_3.gtf 4h_MitoCDNB_4.gtf 4h_MitoCDNB_5.gtf 4h_MitoCDNB_6.gtf 4h_Vehicle_1.gtf 4h_Vehicle_2.gtf 4h_Vehicle_3.gtf 4h_Vehicle_4.gtf 4h_Vehicle_5.gtf 4h_Vehicle_6.gtf 1_Liver_Basal_20.gtf 1_Liver_Low_20.gtf 1_Liver_High_20.gtf 1_Liver_Basal_3h.gtf 1_Liver_Low_3h.gtf 1_Liver_High_3h.gtf 2_Liver_Basal_20.gtf 2_Liver_Low_20.gtf 2_Liver_High_20.gtf 2_Liver_Basal_3h.gtf 2_Liver_Low_3h.gtf 2_Liver_High_3h.gtf 3_Liver_Basal_20.gtf 3_Liver_Low_20.gtf 3_Liver_High_20.gtf 3_Liver_Basal_3h.gtf 3_Liver_Low_3h.gtf 3_Liver_High_3h.gtf 4_Liver_Basal_20.gtf 4_Liver_Low_20.gtf 4_Liver_High_20.gtf 4_Liver_Basal_3h.gtf 4_Liver_Low_3h.gtf 4_Liver_High_3h.gtf 5_Liver_Basal_20.gtf 5_Liver_Low_20.gtf 5_Liver_High_20.gtf 5_Liver_Basal_3h.gtf 6_Liver_Basal_20.gtf 6_Liver_Low_20.gtf 6_Liver_High_20.gtf 6_Liver_Basal_3h.gtf 6_Liver_Low_3h.gtf 6_Liver_High_3h.gtf Old-Cntrl-HTV1.gtf Old-Cntrl-HTV2.gtf Old-Cntrl-HTV3.gtf Old-Cntrl-HTV4.gtf Old-hMANF-HTV1.gtf Old-hMANF-HTV2.gtf Old-hMANF-HTV3.gtf Old-hMANF-HTV4.gtf Yg-Cntrl-HTV2.gtf Yg-Cntrl-HTV4.gtf Yg-hMANF-HTV1.gtf Yg-hMANF-HTV2.gtf Yg-hMANF-HTV3.gtf Yg-hMANF-HTV4.gtf O-O1.gtf O-O2.gtf O-O3.gtf O-O4.gtf O-O5.gtf O_YgHet_1.gtf O_YgHet_2.gtf O_YgHet_3.gtf O_YgHet_4.gtf O_YgHet_5.gtf O_YgWT_1.gtf O_YgWT_2.gtf O_YgWT_3.gtf O_YgWT_4.gtf O_YgWT_5.gtf Yg_Het1.gtf Yg_Het2.gtf Yg_Het3.gtf Yg_Het4.gtf Yg_Het5.gtf Yg_WT1.gtf Yg_WT2.gtf Yg_WT3.gtf Yg_WT4.gtf Yg_WT5.gtf GFP_1347.gtf GFP_1369.gtf GFP_1371.gtf Nudt7_1357.gtf Nudt7_1359.gtf Nudt7_1365.gtf Nudt7_2305.gtf CHOW1.gtf CHOW2.gtf CHOW3.gtf NASH_OA-NO2_1.gtf NASH_OA-NO2_2.gtf NASH_OA-NO2_3.gtf NASH_OA1.gtf NASH_OA2.gtf NASH_OA3.gtf NASH_PEG1.gtf NASH_PEG2.gtf NASH_PEG3.gtf WT_1.gtf WT_2.gtf WT_3.gtf WT_4.gtf MANFHet_1.gtf MANFHet_2.gtf MANFHet_3.gtf MANFHet_4.gtf .gtf Finished copying... Current dir: /scratch/7805251.1.linga running commands... 1_Liver_Basal_20.gtf 1_Liver_Basal_3h.gtf 1_Liver_High_20.gtf 1_Liver_High_3h.gtf 1_Liver_Low_20.gtf 1_Liver_Low_3h.gtf 1h_MitoCDNB_1.gtf 1h_MitoCDNB_2.gtf 1h_MitoCDNB_3.gtf 1h_MitoCDNB_4.gtf 1h_MitoCDNB_5.gtf 1h_MitoCDNB_6.gtf 1h_Vehicle_1.gtf 1h_Vehicle_2.gtf 1h_Vehicle_3.gtf 1h_Vehicle_4.gtf 1h_Vehicle_5.gtf 1h_Vehicle_6.gtf 2_Liver_Basal_20.gtf 2_Liver_Basal_3h.gtf 2_Liver_High_20.gtf 2_Liver_High_3h.gtf 2_Liver_Low_20.gtf 2_Liver_Low_3h.gtf 3_Liver_Basal_20.gtf 3_Liver_Basal_3h.gtf 3_Liver_High_20.gtf 3_Liver_High_3h.gtf 3_Liver_Low_20.gtf 3_Liver_Low_3h.gtf 4_Liver_Basal_20.gtf 4_Liver_Basal_3h.gtf 4_Liver_High_20.gtf 4_Liver_High_3h.gtf 4_Liver_Low_20.gtf 4_Liver_Low_3h.gtf 4h_MitoCDNB_1.gtf 4h_MitoCDNB_2.gtf 4h_MitoCDNB_3.gtf 4h_MitoCDNB_4.gtf 4h_MitoCDNB_5.gtf 4h_MitoCDNB_6.gtf 4h_Vehicle_1.gtf 4h_Vehicle_2.gtf 4h_Vehicle_3.gtf 4h_Vehicle_4.gtf 4h_Vehicle_5.gtf 4h_Vehicle_6.gtf 5_Liver_Basal_20.gtf 5_Liver_Basal_3h.gtf 5_Liver_High_20.gtf 5_Liver_Low_20.gtf 6_Liver_Basal_20.gtf 6_Liver_Basal_3h.gtf 6_Liver_High_20.gtf 6_Liver_High_3h.gtf 6_Liver_Low_20.gtf 6_Liver_Low_3h.gtf APAPL2.gtf APAPL3.gtf CHOW1.gtf CHOW2.gtf CHOW3.gtf GFP_1347.gtf GFP_1369.gtf GFP_1371.gtf I-R-1.gtf I-R-2.gtf I-R-3.gtf IC57-1.gtf IC57-1149.gtf IC57-1150.gtf IC57-1151.gtf IC57-1152.gtf IC57-1159.gtf IC57-1160.gtf IC57-1161.gtf IC57-1162.gtf IC57-1164.gtf IC57-1165.gtf IC57-1166.gtf IC57-1167.gtf IC57-1169.gtf IC57-1170.gtf IC57-1171.gtf IC57-1172.gtf IC57-2.gtf IC57-3.gtf IC57-4.gtf IC57-6.gtf IC57-7.gtf IC57-8.gtf IC57-9.gtf IPO-1.gtf IPO-2.gtf IPO-3.gtf LRH-APAPL1.gtf LRH-APAPL2.gtf MANFHet_1.gtf MANFHet_2.gtf MANFHet_3.gtf MANFHet_4.gtf N-1.gtf N-2.gtf N-3.gtf NASH_OA-NO2_1.gtf NASH_OA-NO2_2.gtf NASH_OA-NO2_3.gtf NASH_OA1.gtf NASH_OA2.gtf NASH_OA3.gtf NASH_PEG1.gtf NASH_PEG2.gtf NASH_PEG3.gtf Nudt7_1357.gtf Nudt7_1359.gtf Nudt7_1365.gtf Nudt7_2305.gtf O-O1.gtf O-O2.gtf O-O3.gtf O-O4.gtf O-O5.gtf O_YgHet_1.gtf O_YgHet_2.gtf O_YgHet_3.gtf O_YgHet_4.gtf O_YgHet_5.gtf O_YgWT_1.gtf O_YgWT_2.gtf O_YgWT_3.gtf O_YgWT_4.gtf O_YgWT_5.gtf Old-Cntrl-HTV1.gtf Old-Cntrl-HTV2.gtf Old-Cntrl-HTV3.gtf Old-Cntrl-HTV4.gtf Old-hMANF-HTV1.gtf Old-hMANF-HTV2.gtf Old-hMANF-HTV3.gtf Old-hMANF-HTV4.gtf PAPL1.gtf Tisha_lncRNAs.gtf VL1.gtf VL2.gtf VL3.gtf WT_1.gtf WT_2.gtf WT_3.gtf WT_4.gtf Yg-Cntrl-HTV2.gtf Yg-Cntrl-HTV4.gtf Yg-hMANF-HTV1.gtf Yg-hMANF-HTV2.gtf Yg-hMANF-HTV3.gtf Yg-hMANF-HTV4.gtf Yg_Het1.gtf Yg_Het2.gtf Yg_Het3.gtf Yg_Het4.gtf Yg_Het5.gtf Yg_WT1.gtf Yg_WT2.gtf Yg_WT3.gtf Yg_WT4.gtf Yg_WT5.gtf assemblies.txt genes.gtf genomeWithRandom.fa [Thu Jul 18 18:17:37 2019] Beginning transcriptome assembly merge ------------------------------------------- [Thu Jul 18 18:17:37 2019] Preparing output location cuffmerge_test_cuffmerge/ Traceback (most recent call last): File "/share/pkg.7/cufflinks/2.2.1/install/bin/cuffmerge", line 580, in sys.exit(main()) File "/share/pkg.7/cufflinks/2.2.1/install/bin/cuffmerge", line 538, in main gtf_input_files = test_input_files(transfrag_list_file) File "/share/pkg.7/cufflinks/2.2.1/install/bin/cuffmerge", line 268, in test_input_files g = open(line,"r") IOError: [Errno 2] No such file or directory: '.gtf' cuffmerge -o cuffmerge_test_cuffmerge -p 2 -g genes.gtf -s genomeWithRandom.fa assemblies.txt done running. copying... List of files in scratch 1_Liver_Basal_20.gtf 1_Liver_Basal_3h.gtf 1_Liver_High_20.gtf 1_Liver_High_3h.gtf 1_Liver_Low_20.gtf 1_Liver_Low_3h.gtf 1h_MitoCDNB_1.gtf 1h_MitoCDNB_2.gtf 1h_MitoCDNB_3.gtf 1h_MitoCDNB_4.gtf 1h_MitoCDNB_5.gtf 1h_MitoCDNB_6.gtf 1h_Vehicle_1.gtf 1h_Vehicle_2.gtf 1h_Vehicle_3.gtf 1h_Vehicle_4.gtf 1h_Vehicle_5.gtf 1h_Vehicle_6.gtf 2_Liver_Basal_20.gtf 2_Liver_Basal_3h.gtf 2_Liver_High_20.gtf 2_Liver_High_3h.gtf 2_Liver_Low_20.gtf 2_Liver_Low_3h.gtf 3_Liver_Basal_20.gtf 3_Liver_Basal_3h.gtf 3_Liver_High_20.gtf 3_Liver_High_3h.gtf 3_Liver_Low_20.gtf 3_Liver_Low_3h.gtf 4_Liver_Basal_20.gtf 4_Liver_Basal_3h.gtf 4_Liver_High_20.gtf 4_Liver_High_3h.gtf 4_Liver_Low_20.gtf 4_Liver_Low_3h.gtf 4h_MitoCDNB_1.gtf 4h_MitoCDNB_2.gtf 4h_MitoCDNB_3.gtf 4h_MitoCDNB_4.gtf 4h_MitoCDNB_5.gtf 4h_MitoCDNB_6.gtf 4h_Vehicle_1.gtf 4h_Vehicle_2.gtf 4h_Vehicle_3.gtf 4h_Vehicle_4.gtf 4h_Vehicle_5.gtf 4h_Vehicle_6.gtf 5_Liver_Basal_20.gtf 5_Liver_Basal_3h.gtf 5_Liver_High_20.gtf 5_Liver_Low_20.gtf 6_Liver_Basal_20.gtf 6_Liver_Basal_3h.gtf 6_Liver_High_20.gtf 6_Liver_High_3h.gtf 6_Liver_Low_20.gtf 6_Liver_Low_3h.gtf APAPL2.gtf APAPL3.gtf CHOW1.gtf CHOW2.gtf CHOW3.gtf GFP_1347.gtf GFP_1369.gtf GFP_1371.gtf I-R-1.gtf I-R-2.gtf I-R-3.gtf IC57-1.gtf IC57-1149.gtf IC57-1150.gtf IC57-1151.gtf IC57-1152.gtf IC57-1159.gtf IC57-1160.gtf IC57-1161.gtf IC57-1162.gtf IC57-1164.gtf IC57-1165.gtf IC57-1166.gtf IC57-1167.gtf IC57-1169.gtf IC57-1170.gtf IC57-1171.gtf IC57-1172.gtf IC57-2.gtf IC57-3.gtf IC57-4.gtf IC57-6.gtf IC57-7.gtf IC57-8.gtf IC57-9.gtf IPO-1.gtf IPO-2.gtf IPO-3.gtf LRH-APAPL1.gtf LRH-APAPL2.gtf MANFHet_1.gtf MANFHet_2.gtf MANFHet_3.gtf MANFHet_4.gtf N-1.gtf N-2.gtf N-3.gtf NASH_OA-NO2_1.gtf NASH_OA-NO2_2.gtf NASH_OA-NO2_3.gtf NASH_OA1.gtf NASH_OA2.gtf NASH_OA3.gtf NASH_PEG1.gtf NASH_PEG2.gtf NASH_PEG3.gtf Nudt7_1357.gtf Nudt7_1359.gtf Nudt7_1365.gtf Nudt7_2305.gtf O-O1.gtf O-O2.gtf O-O3.gtf O-O4.gtf O-O5.gtf O_YgHet_1.gtf O_YgHet_2.gtf O_YgHet_3.gtf O_YgHet_4.gtf O_YgHet_5.gtf O_YgWT_1.gtf O_YgWT_2.gtf O_YgWT_3.gtf O_YgWT_4.gtf O_YgWT_5.gtf Old-Cntrl-HTV1.gtf Old-Cntrl-HTV2.gtf Old-Cntrl-HTV3.gtf Old-Cntrl-HTV4.gtf Old-hMANF-HTV1.gtf Old-hMANF-HTV2.gtf Old-hMANF-HTV3.gtf Old-hMANF-HTV4.gtf PAPL1.gtf Tisha_lncRNAs.gtf VL1.gtf VL2.gtf VL3.gtf WT_1.gtf WT_2.gtf WT_3.gtf WT_4.gtf Yg-Cntrl-HTV2.gtf Yg-Cntrl-HTV4.gtf Yg-hMANF-HTV1.gtf Yg-hMANF-HTV2.gtf Yg-hMANF-HTV3.gtf Yg-hMANF-HTV4.gtf Yg_Het1.gtf Yg_Het2.gtf Yg_Het3.gtf Yg_Het4.gtf Yg_Het5.gtf Yg_WT1.gtf Yg_WT2.gtf Yg_WT3.gtf Yg_WT4.gtf Yg_WT5.gtf assemblies.txt genes.gtf genomeWithRandom.fa cuffmerge_test_cuffmerge: logs tmp Size of files in scratch 72M 1_Liver_Basal_20.gtf 72M 1_Liver_Basal_3h.gtf 77M 1_Liver_High_20.gtf 78M 1_Liver_High_3h.gtf 79M 1_Liver_Low_20.gtf 76M 1_Liver_Low_3h.gtf 85M 1h_MitoCDNB_1.gtf 84M 1h_MitoCDNB_2.gtf 84M 1h_MitoCDNB_3.gtf 85M 1h_MitoCDNB_4.gtf 85M 1h_MitoCDNB_5.gtf 86M 1h_MitoCDNB_6.gtf 86M 1h_Vehicle_1.gtf 86M 1h_Vehicle_2.gtf 85M 1h_Vehicle_3.gtf 85M 1h_Vehicle_4.gtf 85M 1h_Vehicle_5.gtf 86M 1h_Vehicle_6.gtf 77M 2_Liver_Basal_20.gtf 72M 2_Liver_Basal_3h.gtf 72M 2_Liver_High_20.gtf 72M 2_Liver_High_3h.gtf 73M 2_Liver_Low_20.gtf 78M 2_Liver_Low_3h.gtf 78M 3_Liver_Basal_20.gtf 72M 3_Liver_Basal_3h.gtf 78M 3_Liver_High_20.gtf 72M 3_Liver_High_3h.gtf 75M 3_Liver_Low_20.gtf 79M 3_Liver_Low_3h.gtf 72M 4_Liver_Basal_20.gtf 78M 4_Liver_Basal_3h.gtf 81M 4_Liver_High_20.gtf 81M 4_Liver_High_3h.gtf 72M 4_Liver_Low_20.gtf 72M 4_Liver_Low_3h.gtf 85M 4h_MitoCDNB_1.gtf 85M 4h_MitoCDNB_2.gtf 85M 4h_MitoCDNB_3.gtf 85M 4h_MitoCDNB_4.gtf 86M 4h_MitoCDNB_5.gtf 85M 4h_MitoCDNB_6.gtf 85M 4h_Vehicle_1.gtf 84M 4h_Vehicle_2.gtf 85M 4h_Vehicle_3.gtf 86M 4h_Vehicle_4.gtf 85M 4h_Vehicle_5.gtf 84M 4h_Vehicle_6.gtf 77M 5_Liver_Basal_20.gtf 72M 5_Liver_Basal_3h.gtf 79M 5_Liver_High_20.gtf 72M 5_Liver_Low_20.gtf 77M 6_Liver_Basal_20.gtf 72M 6_Liver_Basal_3h.gtf 79M 6_Liver_High_20.gtf 72M 6_Liver_High_3h.gtf 72M 6_Liver_Low_20.gtf 77M 6_Liver_Low_3h.gtf 89M APAPL2.gtf 89M APAPL3.gtf 72M CHOW1.gtf 73M CHOW2.gtf 73M CHOW3.gtf 78M GFP_1347.gtf 79M GFP_1369.gtf 77M GFP_1371.gtf 74M I-R-1.gtf 74M I-R-2.gtf 74M I-R-3.gtf 76M IC57-1.gtf 77M IC57-1149.gtf 76M IC57-1150.gtf 75M IC57-1151.gtf 75M IC57-1152.gtf 77M IC57-1159.gtf 78M IC57-1160.gtf 76M IC57-1161.gtf 77M IC57-1162.gtf 76M IC57-1164.gtf 78M IC57-1165.gtf 76M IC57-1166.gtf 76M IC57-1167.gtf 76M IC57-1169.gtf 76M IC57-1170.gtf 76M IC57-1171.gtf 76M IC57-1172.gtf 77M IC57-2.gtf 78M IC57-3.gtf 73M IC57-4.gtf 75M IC57-6.gtf 78M IC57-7.gtf 77M IC57-8.gtf 75M IC57-9.gtf 73M IPO-1.gtf 73M IPO-2.gtf 73M IPO-3.gtf 90M LRH-APAPL1.gtf 88M LRH-APAPL2.gtf 93M MANFHet_1.gtf 92M MANFHet_2.gtf 91M MANFHet_3.gtf 93M MANFHet_4.gtf 74M N-1.gtf 75M N-2.gtf 74M N-3.gtf 74M NASH_OA-NO2_1.gtf 75M NASH_OA-NO2_2.gtf 73M NASH_OA-NO2_3.gtf 73M NASH_OA1.gtf 73M NASH_OA2.gtf 73M NASH_OA3.gtf 74M NASH_PEG1.gtf 74M NASH_PEG2.gtf 73M NASH_PEG3.gtf 78M Nudt7_1357.gtf 74M Nudt7_1359.gtf 77M Nudt7_1365.gtf 78M Nudt7_2305.gtf 90M O-O1.gtf 91M O-O2.gtf 92M O-O3.gtf 90M O-O4.gtf 92M O-O5.gtf 89M O_YgHet_1.gtf 90M O_YgHet_2.gtf 90M O_YgHet_3.gtf 89M O_YgHet_4.gtf 90M O_YgHet_5.gtf 91M O_YgWT_1.gtf 91M O_YgWT_2.gtf 91M O_YgWT_3.gtf 90M O_YgWT_4.gtf 90M O_YgWT_5.gtf 90M Old-Cntrl-HTV1.gtf 90M Old-Cntrl-HTV2.gtf 90M Old-Cntrl-HTV3.gtf 91M Old-Cntrl-HTV4.gtf 90M Old-hMANF-HTV1.gtf 89M Old-hMANF-HTV2.gtf 89M Old-hMANF-HTV3.gtf 90M Old-hMANF-HTV4.gtf 90M PAPL1.gtf 266M Tisha_lncRNAs.gtf 88M VL1.gtf 87M VL2.gtf 88M VL3.gtf 92M WT_1.gtf 92M WT_2.gtf 92M WT_3.gtf 91M WT_4.gtf 89M Yg-Cntrl-HTV2.gtf 88M Yg-Cntrl-HTV4.gtf 89M Yg-hMANF-HTV1.gtf 88M Yg-hMANF-HTV2.gtf 83M Yg-hMANF-HTV3.gtf 90M Yg-hMANF-HTV4.gtf 89M Yg_Het1.gtf 89M Yg_Het2.gtf 90M Yg_Het3.gtf 90M Yg_Het4.gtf 89M Yg_Het5.gtf 90M Yg_WT1.gtf 90M Yg_WT2.gtf 90M Yg_WT3.gtf 90M Yg_WT4.gtf 90M Yg_WT5.gtf 4.0K assemblies.txt 4.0K cuffmerge_test_cuffmerge/tmp 8.0K cuffmerge_test_cuffmerge/logs 16K cuffmerge_test_cuffmerge 81M genes.gtf 2.6G genomeWithRandom.fa 16G total Stop time is Thu Jul 18 18:17:38 EDT 2019