/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Removing ../09d_DE_2_RefSeqLncRNA76k
Removing ../09d_DE_3_RefSeqLncRNA76k
Removing ../09d_DE_1_RefSeqLncRNA76k
Creating ../09d_DE_1_RefSeqLncRNA76k
Creating ../09d_DE_2_RefSeqLncRNA76k
Creating ../09d_DE_3_RefSeqLncRNA76k
Diff.ex directories are generated
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
running full pipeline
Start: 01

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
INFO: G221_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M69 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G221_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M70 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G221_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M71 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G221_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M72 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G221_M73 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M73 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G221_M74 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M74 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G221_M75 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M75 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G221_M76 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M76 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G221_M77 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M77 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G221_M78 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M78 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G221_M79 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M79 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G221_M80 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M80 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M61 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M61 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M62 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M62 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M63 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M63 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M64 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M64 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M65 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M65 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M66 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M66 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M67 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M67 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M68 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M68 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M69 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M70 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M71 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
INFO: G216_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M72 /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples
End of 01_Copy_Samples commands
-----------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 0 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/01_Copy_Samples /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Done: Step_01_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 01

 -------------------------Start: 02

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Skip recalculation for G221_M69 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M70 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M71 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M72 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M73 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M74 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M75 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M76 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M77 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M78 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M79 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M80 sample. Results already obtained and FULL_RECALC flag set to 0.
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M61 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M61
Your job 4869089 ("Step_02_G221_RNASEQ_MS316_G216_M61") has been submitted
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M62 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M62
Your job 4869091 ("Step_02_G221_RNASEQ_MS316_G216_M62") has been submitted
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M63 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M63
Your job 4869093 ("Step_02_G221_RNASEQ_MS316_G216_M63") has been submitted
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M64 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M64
Your job 4869095 ("Step_02_G221_RNASEQ_MS316_G216_M64") has been submitted
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M65 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M65
Your job 4869097 ("Step_02_G221_RNASEQ_MS316_G216_M65") has been submitted
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M66 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M66
Your job 4869099 ("Step_02_G221_RNASEQ_MS316_G216_M66") has been submitted
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M67 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M67
Your job 4869101 ("Step_02_G221_RNASEQ_MS316_G216_M67") has been submitted
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M68 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M68
Your job 4869103 ("Step_02_G221_RNASEQ_MS316_G216_M68") has been submitted
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M69 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M69
Your job 4869105 ("Step_02_G221_RNASEQ_MS316_G216_M69") has been submitted
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M70 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M70
Your job 4869107 ("Step_02_G221_RNASEQ_MS316_G216_M70") has been submitted
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M71 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M71
Your job 4869109 ("Step_02_G221_RNASEQ_MS316_G216_M71") has been submitted
+ qsub -N Step_02_G221_RNASEQ_MS316_G216_M72 -P wax-es -l h_rt=00:15:00 Read_Strandness.qsub G216_M72
Your job 4869111 ("Step_02_G221_RNASEQ_MS316_G216_M72") has been submitted
End of 05_READ_STRANDEDNESS commands
-----------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 12 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Summarise results...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M69/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M69_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M70/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M70_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M71/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M71_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M72/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M72_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M73/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M73_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M74/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M74_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M75/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M75_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M76/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M76_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M77/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M77_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M78/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M78_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M79/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M79_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G221_M80/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G221_M80_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M61/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M61_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M62/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M62_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M63/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M63_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M64/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M64_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M65/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M65_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M66/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M66_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M67/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M67_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M68/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M68_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M69/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M69_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M70/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M70_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M71/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M71_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
/projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES/G216_M72/Read_Strandness /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
+ cat G216_M72_Read_Strandness.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/02_Read_Strandness
--------------------
Done: Step_02_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 02

 -------------------------Start: 03

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/03_FASTQC /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Recalculation is not required. FULL_RECALC set to 0.
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 0 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/03_FASTQC /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Summarise results...
Recalculation is not required. FULL_RECALC set to 0.
Done: Step_03_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 03

 -------------------------Start: 04

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/04_TopHat_Paired_End /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Skip recalculation for G221_M69 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M70 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M71 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M72 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M73 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M74 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M75 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M76 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M77 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M78 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M79 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G221_M80 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M61 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M62 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M63 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M64 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M65 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M66 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M67 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M68 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M69 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M70 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M71 sample. Results already obtained and FULL_RECALC flag set to 0.
Skip recalculation for G216_M72 sample. Results already obtained and FULL_RECALC flag set to 0.
End of TOPHAT commands
-----------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 0 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/04_TopHat_Paired_End /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Summarise results...
Recalculation is not required. FULL_RECALC set to 0.
Done: Step_04_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 04

 -------------------------Start: 06

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/06_CollectMetrics /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Recalculation is not required. FULL_RECALC set to 0.
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 0 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/06_CollectMetrics /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Summarise results...
Recalculation is not required. FULL_RECALC set to 0.
Done: Step_06_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 06

 -------------------------Start: 08

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/08_Extract_Counts /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Skip recalculation for G221_M69 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M69 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
Skip recalculation for G221_M70 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M70 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
Skip recalculation for G221_M71 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M71 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
Skip recalculation for G221_M72 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M72 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
Skip recalculation for G221_M73 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M73 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
Skip recalculation for G221_M74 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M74 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
Skip recalculation for G221_M75 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M75 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
Skip recalculation for G221_M76 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M76 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
Skip recalculation for G221_M77 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M77 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
Skip recalculation for G221_M78 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M78 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
Skip recalculation for G221_M79 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M79 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
Skip recalculation for G221_M80 sample for dir RefSeqLncRNA76k_FullGeneBody_GTF. Results already obtained.
Skip recalculation for G221_M80 sample for dir RefSeqLncRNA76k_ExonCollapsed_GTF. Results already obtained.
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M61 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M61 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870425 ("Step_08_G221_RNASEQ_MS316_G216_M61") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M61 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M61 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870426 ("Step_08_G221_RNASEQ_MS316_G216_M61") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M62 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M62 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870427 ("Step_08_G221_RNASEQ_MS316_G216_M62") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M62 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M62 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870428 ("Step_08_G221_RNASEQ_MS316_G216_M62") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M63 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M63 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870429 ("Step_08_G221_RNASEQ_MS316_G216_M63") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M63 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M63 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870430 ("Step_08_G221_RNASEQ_MS316_G216_M63") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M64 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M64 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870431 ("Step_08_G221_RNASEQ_MS316_G216_M64") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M64 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M64 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870432 ("Step_08_G221_RNASEQ_MS316_G216_M64") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M65 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M65 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870433 ("Step_08_G221_RNASEQ_MS316_G216_M65") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M65 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M65 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870434 ("Step_08_G221_RNASEQ_MS316_G216_M65") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M66 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M66 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870435 ("Step_08_G221_RNASEQ_MS316_G216_M66") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M66 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M66 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870436 ("Step_08_G221_RNASEQ_MS316_G216_M66") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M67 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M67 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870437 ("Step_08_G221_RNASEQ_MS316_G216_M67") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M67 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M67 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870438 ("Step_08_G221_RNASEQ_MS316_G216_M67") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M68 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M68 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870439 ("Step_08_G221_RNASEQ_MS316_G216_M68") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M68 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M68 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870440 ("Step_08_G221_RNASEQ_MS316_G216_M68") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M69 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M69 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870441 ("Step_08_G221_RNASEQ_MS316_G216_M69") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M69 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M69 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870442 ("Step_08_G221_RNASEQ_MS316_G216_M69") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M70 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M70 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870443 ("Step_08_G221_RNASEQ_MS316_G216_M70") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M70 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M70 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870444 ("Step_08_G221_RNASEQ_MS316_G216_M70") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M71 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M71 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870445 ("Step_08_G221_RNASEQ_MS316_G216_M71") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M71 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M71 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870446 ("Step_08_G221_RNASEQ_MS316_G216_M71") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M72 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M72 08_RefSeqLncRNA76k_FullGeneBody.gtf featureCounts
Your job 4870447 ("Step_08_G221_RNASEQ_MS316_G216_M72") has been submitted
+ qsub -N Step_08_G221_RNASEQ_MS316_G216_M72 -P wax-es -l h_rt=24:00:00 Extract_Counts.qsub G216_M72 09_RefSeqLncRNA76k_ExonCollapsed.gtf featureCounts
Your job 4870448 ("Step_08_G221_RNASEQ_MS316_G216_M72") has been submitted
End of 8 step commands
-----------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 24 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/08_Extract_Counts /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Summarise results...
Recalculation is not required. FULL_RECALC set to 0.
Done: Step_08_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 08

 -------------------------Start: 09d

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_2_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
+ qsub -N Step_09d_G221_RNASEQ_MS316_DiffExp_2i -P wax-es -l h_rt=01:00:00 DiffExp.qsub /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_2_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES G221_RNASEQ_MS316 /projectnb/wax-es/routines/GTF_Files_default 09_RefSeqLncRNA76k_ExonCollapsed.gtf Male_liver_8wk_G216 Male_liver_15wk_MS316 /projectnb/wax-es/routines/GTF_Files_default/lengths 09_RefSeqLncRNA76k_ExonCollapsed_lengths.txt RefSeqLncRNA76k_ExonCollapsed_GTF DiffExp_v2_RefSeqLncRNA76k_ExonCollapsed DiffExp_2i RefSeqLncRNA76k_ExonCollapsed featureCounts
Your job 4870654 ("Step_09d_G221_RNASEQ_MS316_DiffExp_2i") has been submitted
+ qsub -N Step_09d_G221_RNASEQ_MS316_DiffExp_2h -P wax-es -l h_rt=01:00:00 DiffExp.qsub /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_2_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES G221_RNASEQ_MS316 /projectnb/wax-es/routines/GTF_Files_default 08_RefSeqLncRNA76k_FullGeneBody.gtf Male_liver_8wk_G216 Male_liver_15wk_MS316 /projectnb/wax-es/routines/GTF_Files_default/lengths 08_RefSeqLncRNA76k_FullGeneBody_lengths.txt RefSeqLncRNA76k_FullGeneBody_GTF DiffExp_v2_RefSeqLncRNA76k_FullGeneBody DiffExp_2h RefSeqLncRNA76k_FullGeneBody featureCounts
Your job 4870655 ("Step_09d_G221_RNASEQ_MS316_DiffExp_2h") has been submitted
End of qsub commands
-----------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_3_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
+ qsub -N Step_09d_G221_RNASEQ_MS316_DiffExp_3i -P wax-es -l h_rt=01:00:00 DiffExp.qsub /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_3_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES G221_RNASEQ_MS316 /projectnb/wax-es/routines/GTF_Files_default 09_RefSeqLncRNA76k_ExonCollapsed.gtf Female_liver_8wk_G216 Female_liver_15wk_MS316 /projectnb/wax-es/routines/GTF_Files_default/lengths 09_RefSeqLncRNA76k_ExonCollapsed_lengths.txt RefSeqLncRNA76k_ExonCollapsed_GTF DiffExp_v2_RefSeqLncRNA76k_ExonCollapsed DiffExp_3i RefSeqLncRNA76k_ExonCollapsed featureCounts
Your job 4870656 ("Step_09d_G221_RNASEQ_MS316_DiffExp_3i") has been submitted
+ qsub -N Step_09d_G221_RNASEQ_MS316_DiffExp_3h -P wax-es -l h_rt=01:00:00 DiffExp.qsub /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_3_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES G221_RNASEQ_MS316 /projectnb/wax-es/routines/GTF_Files_default 08_RefSeqLncRNA76k_FullGeneBody.gtf Female_liver_8wk_G216 Female_liver_15wk_MS316 /projectnb/wax-es/routines/GTF_Files_default/lengths 08_RefSeqLncRNA76k_FullGeneBody_lengths.txt RefSeqLncRNA76k_FullGeneBody_GTF DiffExp_v2_RefSeqLncRNA76k_FullGeneBody DiffExp_3h RefSeqLncRNA76k_FullGeneBody featureCounts
Your job 4870657 ("Step_09d_G221_RNASEQ_MS316_DiffExp_3h") has been submitted
End of qsub commands
-----------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_1_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
+ qsub -N Step_09d_G221_RNASEQ_MS316_DiffExp_1h -P wax-es -l h_rt=01:00:00 DiffExp.qsub /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_1_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES G221_RNASEQ_MS316 /projectnb/wax-es/routines/GTF_Files_default 08_RefSeqLncRNA76k_FullGeneBody.gtf Female_liver_15wk_MS316 Male_liver_15wk_MS316 /projectnb/wax-es/routines/GTF_Files_default/lengths 08_RefSeqLncRNA76k_FullGeneBody_lengths.txt RefSeqLncRNA76k_FullGeneBody_GTF DiffExp_v2_RefSeqLncRNA76k_FullGeneBody DiffExp_1h RefSeqLncRNA76k_FullGeneBody featureCounts
Your job 4870658 ("Step_09d_G221_RNASEQ_MS316_DiffExp_1h") has been submitted
+ qsub -N Step_09d_G221_RNASEQ_MS316_DiffExp_1i -P wax-es -l h_rt=01:00:00 DiffExp.qsub /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_1_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES G221_RNASEQ_MS316 /projectnb/wax-es/routines/GTF_Files_default 09_RefSeqLncRNA76k_ExonCollapsed.gtf Female_liver_15wk_MS316 Male_liver_15wk_MS316 /projectnb/wax-es/routines/GTF_Files_default/lengths 09_RefSeqLncRNA76k_ExonCollapsed_lengths.txt RefSeqLncRNA76k_ExonCollapsed_GTF DiffExp_v2_RefSeqLncRNA76k_ExonCollapsed DiffExp_1i RefSeqLncRNA76k_ExonCollapsed featureCounts
Your job 4870659 ("Step_09d_G221_RNASEQ_MS316_DiffExp_1i") has been submitted
End of qsub commands
-----------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 6 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_2_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Summarise results...

Loading required modules...

Male_liver_15wk_MS316.G221_M69M70M71M72M73M74.Male_liver_8wk_G216.G216_M61M62M63M64M65M66.DiffExp_v2
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_2_RefSeqLncRNA76k/Summary_Differential_Expression /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_2_RefSeqLncRNA76k
./2_Male_liver_15wk_MS316_G221_M69M70M71M72M73M74_vs_Male_liver_8wk_G216_G216_M61M62M63M64M65M66_DiffExp_v2_RefSeqLncRNA76k_ExonCollapsed_forSEGEXUpload_FPKM_DESeq_featureCounts.txt
./2_Male_liver_15wk_MS316_G221_M69M70M71M72M73M74_vs_Male_liver_8wk_G216_G216_M61M62M63M64M65M66_DiffExp_v2_RefSeqLncRNA76k_ExonCollapsed_forSEGEXUpload_TPM_DESeq_featureCounts.txt ./2_Male_liver_15wk_MS316_G221_M69M70M71M72M73M74_vs_Male_liver_8wk_G216_G216_M61M62M63M64M65M66_DiffExp_v2_RefSeqLncRNA76k_FullGeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt
./2_Male_liver_15wk_MS316_G221_M69M70M71M72M73M74_vs_Male_liver_8wk_G216_G216_M61M62M63M64M65M66_DiffExp_v2_RefSeqLncRNA76k_FullGeneBody_forSEGEXUpload_FPKM_DESeq_featureCounts.txt   > /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_2_RefSeqLncRNA76k/Summary_Differential_Expression/SEGEX_Upload_Files/Combined/2_Combined_forSEGEXUpload_DESeq.featureCounts.Male_liver_15wk_MS316.G221_M69M70M71M72M73M74.Male_liver_8wk_G216.G216_M61M62M63M64M65M66.DiffExp_v2.txt
Running paste command
Running paste command
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_2_RefSeqLncRNA76k
Output_DiffExp_2h_featureCounts_RefSeqLncRNA76k_FullGeneBody
Count for Up_Genes_DESeq_*.txt
Count for Down_Genes_DESeq_*.txt
Print to output file
Count for Up_Genes_EdgeR_*.txt
Count for Down_Genes_EdgeR_*.txt
Print to OUTPUT_TABLE
Print to OUTPUT_TABLE_2
Copy Down_Genes*.txt and Up_Genes*.txt files to DE_Text_DIR
Output_DiffExp_2i_featureCounts_RefSeqLncRNA76k_ExonCollapsed
Count for Up_Genes_DESeq_*.txt
Count for Down_Genes_DESeq_*.txt
Print to output file
Count for Up_Genes_EdgeR_*.txt
Count for Down_Genes_EdgeR_*.txt
Print to OUTPUT_TABLE
Print to OUTPUT_TABLE_2
Copy Down_Genes*.txt and Up_Genes*.txt files to DE_Text_DIR
#--------------------------------------------------------------------------
Check out /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_2_RefSeqLncRNA76k/Summary_Differential_Expression
#--------------------------------------------------------------------------
Done: Step_09d_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_3_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Summarise results...

Loading required modules...

Female_liver_15wk_MS316.G221_M75M76M77M78M79M80.Female_liver_8wk_G216.G216_M67M68M69M70M71M72.DiffExp_v2
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_3_RefSeqLncRNA76k/Summary_Differential_Expression /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_3_RefSeqLncRNA76k
./3_Female_liver_15wk_MS316_G221_M75M76M77M78M79M80_vs_Female_liver_8wk_G216_G216_M67M68M69M70M71M72_DiffExp_v2_RefSeqLncRNA76k_ExonCollapsed_forSEGEXUpload_FPKM_DESeq_featureCounts.txt
./3_Female_liver_15wk_MS316_G221_M75M76M77M78M79M80_vs_Female_liver_8wk_G216_G216_M67M68M69M70M71M72_DiffExp_v2_RefSeqLncRNA76k_ExonCollapsed_forSEGEXUpload_TPM_DESeq_featureCounts.txt ./3_Female_liver_15wk_MS316_G221_M75M76M77M78M79M80_vs_Female_liver_8wk_G216_G216_M67M68M69M70M71M72_DiffExp_v2_RefSeqLncRNA76k_FullGeneBody_forSEGEXUpload_FPKM_DESeq_featureCounts.txt
./3_Female_liver_15wk_MS316_G221_M75M76M77M78M79M80_vs_Female_liver_8wk_G216_G216_M67M68M69M70M71M72_DiffExp_v2_RefSeqLncRNA76k_FullGeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt   > /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_3_RefSeqLncRNA76k/Summary_Differential_Expression/SEGEX_Upload_Files/Combined/3_Combined_forSEGEXUpload_DESeq.featureCounts.Female_liver_15wk_MS316.G221_M75M76M77M78M79M80.Female_liver_8wk_G216.G216_M67M68M69M70M71M72.DiffExp_v2.txt
Running paste command
Running paste command
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_3_RefSeqLncRNA76k
Output_DiffExp_3h_featureCounts_RefSeqLncRNA76k_FullGeneBody
Count for Up_Genes_DESeq_*.txt
Count for Down_Genes_DESeq_*.txt
Print to output file
Count for Up_Genes_EdgeR_*.txt
Count for Down_Genes_EdgeR_*.txt
Print to OUTPUT_TABLE
Print to OUTPUT_TABLE_2
Copy Down_Genes*.txt and Up_Genes*.txt files to DE_Text_DIR
Output_DiffExp_3i_featureCounts_RefSeqLncRNA76k_ExonCollapsed
Count for Up_Genes_DESeq_*.txt
Count for Down_Genes_DESeq_*.txt
Print to output file
Count for Up_Genes_EdgeR_*.txt
Count for Down_Genes_EdgeR_*.txt
Print to OUTPUT_TABLE
Print to OUTPUT_TABLE_2
Copy Down_Genes*.txt and Up_Genes*.txt files to DE_Text_DIR
#--------------------------------------------------------------------------
Check out /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_3_RefSeqLncRNA76k/Summary_Differential_Expression
#--------------------------------------------------------------------------
Done: Step_09d_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_1_RefSeqLncRNA76k /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Summarise results...

Loading required modules...

Male_liver_15wk_MS316.G221_M69M70M71M72M73M74.Female_liver_15wk_MS316.G221_M75M76M77M78M79M80.DiffExp_v2
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_1_RefSeqLncRNA76k/Summary_Differential_Expression /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_1_RefSeqLncRNA76k
./1_Male_liver_15wk_MS316_G221_M69M70M71M72M73M74_vs_Female_liver_15wk_MS316_G221_M75M76M77M78M79M80_DiffExp_v2_RefSeqLncRNA76k_ExonCollapsed_forSEGEXUpload_FPKM_DESeq_featureCounts.txt
./1_Male_liver_15wk_MS316_G221_M69M70M71M72M73M74_vs_Female_liver_15wk_MS316_G221_M75M76M77M78M79M80_DiffExp_v2_RefSeqLncRNA76k_ExonCollapsed_forSEGEXUpload_TPM_DESeq_featureCounts.txt ./1_Male_liver_15wk_MS316_G221_M69M70M71M72M73M74_vs_Female_liver_15wk_MS316_G221_M75M76M77M78M79M80_DiffExp_v2_RefSeqLncRNA76k_FullGeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt
./1_Male_liver_15wk_MS316_G221_M69M70M71M72M73M74_vs_Female_liver_15wk_MS316_G221_M75M76M77M78M79M80_DiffExp_v2_RefSeqLncRNA76k_FullGeneBody_forSEGEXUpload_FPKM_DESeq_featureCounts.txt   > /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_1_RefSeqLncRNA76k/Summary_Differential_Expression/SEGEX_Upload_Files/Combined/1_Combined_forSEGEXUpload_DESeq.featureCounts.Male_liver_15wk_MS316.G221_M69M70M71M72M73M74.Female_liver_15wk_MS316.G221_M75M76M77M78M79M80.DiffExp_v2.txt
Running paste command
Running paste command
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_1_RefSeqLncRNA76k
Output_DiffExp_1h_featureCounts_RefSeqLncRNA76k_FullGeneBody
Count for Up_Genes_DESeq_*.txt
Count for Down_Genes_DESeq_*.txt
Print to output file
Count for Up_Genes_EdgeR_*.txt
Count for Down_Genes_EdgeR_*.txt
Print to OUTPUT_TABLE
Print to OUTPUT_TABLE_2
Copy Down_Genes*.txt and Up_Genes*.txt files to DE_Text_DIR
Output_DiffExp_1i_featureCounts_RefSeqLncRNA76k_ExonCollapsed
Count for Up_Genes_DESeq_*.txt
Count for Down_Genes_DESeq_*.txt
Print to output file
Count for Up_Genes_EdgeR_*.txt
Count for Down_Genes_EdgeR_*.txt
Print to OUTPUT_TABLE
Print to OUTPUT_TABLE_2
Copy Down_Genes*.txt and Up_Genes*.txt files to DE_Text_DIR
#--------------------------------------------------------------------------
Check out /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/09d_DE_1_RefSeqLncRNA76k/Summary_Differential_Expression
#--------------------------------------------------------------------------
Done: Step_09d_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 09d

 -------------------------Start: 10

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/10_TACO /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
TACO_ENABLE=0. Step is not required.
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 0 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/10_TACO /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
WARNING: logs directory does not exist. Analysis of logs will not be produced
Summarise results...
TACO_ENABLE=0. Step is not required.
Done: Step_10_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 10

 -------------------------Start: 11

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
INFO: G221_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M73 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M74 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M75 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M76 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M77 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M78 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M79 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M80 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M61 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M62 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M63 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M64 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M65 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M66 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M67 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M68 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Checking availability of G221_M69M70M71M72M73M74 combined files inside the /net/waxman-server/mnt/data/waxmanlabvm_home/TRACKS//INDEXED_PROJECTS/G221
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Checking availability of G221_M75M76M77M78M79M80 combined files inside the /net/waxman-server/mnt/data/waxmanlabvm_home/TRACKS//INDEXED_PROJECTS/G221
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Checking availability of G216_M61M62M63M64M65M66 combined files inside the /net/waxman-server/mnt/data/waxmanlabvm_home/TRACKS//INDEXED_PROJECTS/G216
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Auto: 1
Checking availability of G216_M67M68M69M70M71M72 combined files inside the /net/waxman-server/mnt/data/waxmanlabvm_home/TRACKS//INDEXED_PROJECTS/G216
-----------------------
Start of variable list:
-----------------------
SCRIPT_DIR:
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig
DATASET_LABEL:
G221_RNASEQ_MS316
BU_USER:
mpyatkov
-----------------------
End of variable list
-----------------------
Start *_Tracks_PileUp.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig/UCSC_Track_Lines/G221_RNASEQ_MS316_Tracks_PileUp.txt
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
INFO: G221_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M73 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M74 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M75 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M76 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M77 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M78 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M79 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M80 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M61 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M62 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M63 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M64 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M65 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M66 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M67 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M68 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
Start *_Tracks_Wiggle_240.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig/UCSC_Track_Lines/G221_RNASEQ_MS316_Tracks_Wiggle_240.txt
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
INFO: G221_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M73 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M74 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M75 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M76 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M77 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M78 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M79 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M80 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M61 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M62 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M63 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M64 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M65 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M66 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M67 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M68 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
Start *_Tracks_Wiggle_4.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig/UCSC_Track_Lines/G221_RNASEQ_MS316_Tracks_Wiggle_4.txt
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
INFO: G221_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M73 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M74 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M75 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M76 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M77 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M78 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M79 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M80 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M61 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M62 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M63 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M64 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M65 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M66 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M67 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M68 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig/UCSC_Track_Lines/G221_RNASEQ_MS316_Tracks_Wiggle_12.txt
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
INFO: G221_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M73 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M74 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M75 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M76 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M77 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M78 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M79 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M80 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M61 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M62 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M63 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M64 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M65 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M66 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M67 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M68 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig/UCSC_Track_Lines/G221_RNASEQ_MS316_Tracks_Wiggle_60.txt
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
INFO: G221_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M73 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M74 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M75 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M76 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M77 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M78 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M79 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M80 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M61 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M62 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M63 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M64 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M65 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M66 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M67 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M68 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
Start *_Tracks_Wiggle_autoON.txt
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig/UCSC_Track_Lines/G221_RNASEQ_MS316_Tracks_Wiggle_autoON.txt
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
INFO: G221_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M73 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M74 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M75 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M76 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M77 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M78 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M79 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M80 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M61 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M62 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M63 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M64 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M65 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M66 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M67 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M68 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
Start chromatin state tracks
End chromatin state tracks
Start Tisha_Gene_Definition track
End Tisha_Gene_Definition track
Start BED files of counting regions track(s)
End BED files of counting regions track(s)
Add BAM and BigWig file tracks
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig/UCSC_Track_Lines /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig
#--------------------------------------------------------------------------
Check out /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig/UCSC_Track_Lines or /net/waxman-server/mnt/data/waxmanlabvm_home/TRACKS//PERSONAL/mpyatkov/G221_RNASEQ_MS316
#--------------------------------------------------------------------------
End of qsub commands
-----------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 0 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/11_UCSC_BigWig /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Done: Step_11_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 11

 -------------------------Start: 12

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/12_Venn /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
WARNING: venn_config file is empty. This step will be skipped.
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 0 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/12_Venn /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
WARNING: logs directory does not exist. Analysis of logs will not be produced
Done: Step_12_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 12

 -------------------------Start: 13

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/13_Correlation /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
+ qsub -N Step_13_G221_RNASEQ_MS316_09d -P wax-es -l h_rt=04:00:00 correlation.qsub 09d
Your job 4870695 ("Step_13_G221_RNASEQ_MS316_09d") has been submitted
End of 13_Correlation
-----------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 1 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/13_Correlation /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Done: Step_13_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 13

 -------------------------Start: 14

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
Script_Directory
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
Level_UP:
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
removing '*bam' files
removing '*bai' files
removing '*cram' files
removing '*crai' files
cp: cannot stat '/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/03_FASTQC/Job_Summary/number_of_unique_reads.csv': No such file or directory
cp: cannot stat '/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/12_Venn/Job_Summary/*.pdf': No such file or directory
copy_feature: 09d ExonCollapsed
copy_feature: 09d FullGeneBody
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary/09d_ExonCollapsed_TPM /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary/09d_FullGeneBody_TPM /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary/09d_ExonCollapsed_FPKM /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary/09d_FullGeneBody_FPKM /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary/output/Segex_09d /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
+ Rscript add_segex_index.R 123 0

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Warning message:
Execution is not required. SEGEX_FEATURE_SORT_IX equal to 0 or > 3. SEGEX files will not be renamed. 
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary/09d_DE_Genes_counts /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Male_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_ExonCollapsed = col_character(),
  ratio.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  foldChange.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  padj.RefSeqLncRNA76k_ExonCollapsed = col_double(),
  pval.RefSeqLncRNA76k_ExonCollapsed = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  id.RefSeqLncRNA76k_FullGeneBody = col_character(),
  ratio.RefSeqLncRNA76k_FullGeneBody = col_double(),
  foldChange.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_8wk_G216.RefSeqLncRNA76k_FullGeneBody = col_double(),
  tpm_mean_Female_liver_15wk_MS316.RefSeqLncRNA76k_FullGeneBody = col_double(),
  padj.RefSeqLncRNA76k_FullGeneBody = col_double(),
  pval.RefSeqLncRNA76k_FullGeneBody = col_double()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  Comparison_Number = col_double(),
  Condition_1 = col_character(),
  Condition_2 = col_character()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  Group = col_character(),
  Condition_Name = col_character(),
  Sample_ID = col_character(),
  Description = col_character(),
  Color = col_character()
)

Joining, by = "comparison"
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
Extracting headers from corresponding FASTQ files
INFO: G221_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M73 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M74 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M75 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M76 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M77 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M78 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M79 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G221_M80 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M61 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M62 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M63 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M64 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M65 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M66 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M67 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M68 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M69 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M70 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M71 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
INFO: G216_M72 found in /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/00_Setup_Pipeline/G221_index.csv
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary/G221_RNASEQ_MS316_multiqc_report /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.20 now available!
|           multiqc | Search path : /projectnb/wax-dk/max/G221_RNASEQ_MS316/SAMPLES
|           multiqc | Search path : /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/03_FASTQC
|           multiqc | Search path : /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/06_CollectMetrics
|             rseqc | Found 24 infer_experiment reports
|    feature_counts | Found 24 reports
|            picard | Found 12 InsertSizeMetrics reports
|            picard | Found 12 RnaSeqMetrics reports
|          samtools | Found 37 flagstat reports
|              star | Found 12 reports
|             fastp | Found 12 reports
|            fastqc | Found 24 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : multiqc_report.html
|           multiqc | Data        : multiqc_data
|           multiqc | MultiQC complete
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary
+ Rscript ./Scripts/aggregate_counts.R ../ ./output/G221_RNASEQ_MS316_counts_summary.xlsx

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


── Column specification ────────────────────────────────────────────────────────
cols(
  Group = col_character(),
  Condition_Name = col_character(),
  Sample_ID = col_character(),
  Description = col_character(),
  Color = col_character()
)


── Column specification ────────────────────────────────────────────────────────
cols(
  .default = col_double(),
  id = col_character()
)
ℹ Use `spec()` for the full column specifications.

New names:
* id -> id...1
* id -> id...10
* id -> id...19
* id -> id...20

── Column specification ────────────────────────────────────────────────────────
cols(
  .default = col_double(),
  id = col_character()
)
ℹ Use `spec()` for the full column specifications.

New names:
* id -> id...1
* id -> id...10
* id -> id...11
* id -> id...20

── Column specification ────────────────────────────────────────────────────────
cols(
  .default = col_double(),
  id = col_character()
)
ℹ Use `spec()` for the full column specifications.

New names:
* id -> id...1
* id -> id...2
* id -> id...11
* id -> id...12
Joining, by = c("id", "A_Male_liver_15wk_MS316_G221_M69", "A_Male_liver_15wk_MS316_G221_M70", "A_Male_liver_15wk_MS316_G221_M71", "A_Male_liver_15wk_MS316_G221_M72", "A_Male_liver_15wk_MS316_G221_M73", "A_Male_liver_15wk_MS316_G221_M74", "A_rpkm_mean_Male_liver_15wk_MS316", "A_tpm_mean_Male_liver_15wk_MS316")
Joining, by = c("id", "B_Female_liver_15wk_MS316_G221_M75", "B_Female_liver_15wk_MS316_G221_M76", "B_Female_liver_15wk_MS316_G221_M77", "B_Female_liver_15wk_MS316_G221_M78", "B_Female_liver_15wk_MS316_G221_M79", "B_Female_liver_15wk_MS316_G221_M80", "B_rpkm_mean_Female_liver_15wk_MS316", "B_tpm_mean_Female_liver_15wk_MS316")
Warning messages:
1: Unknown columns: `Male_liver_8wk_G216_G216_M61`, `Male_liver_8wk_G216_G216_M62`, `Male_liver_8wk_G216_G216_M63`, `Male_liver_8wk_G216_G216_M64`, `Male_liver_8wk_G216_G216_M65`, `Male_liver_8wk_G216_G216_M66` 
2: Unknown columns: `Female_liver_8wk_G216_G216_M67`, `Female_liver_8wk_G216_G216_M68`, `Female_liver_8wk_G216_G216_M69`, `Female_liver_8wk_G216_G216_M70`, `Female_liver_8wk_G216_G216_M71`, `Female_liver_8wk_G216_G216_M72` 
3: Unknown columns: `Female_liver_15wk_MS316_G221_M75`, `Female_liver_15wk_MS316_G221_M76`, `Female_liver_15wk_MS316_G221_M77`, `Female_liver_15wk_MS316_G221_M78`, `Female_liver_15wk_MS316_G221_M79`, `Female_liver_15wk_MS316_G221_M80` 
4: Unknown columns: `Female_liver_8wk_G216_G216_M67`, `Female_liver_8wk_G216_G216_M68`, `Female_liver_8wk_G216_G216_M69`, `Female_liver_8wk_G216_G216_M70`, `Female_liver_8wk_G216_G216_M71`, `Female_liver_8wk_G216_G216_M72` 
5: Unknown columns: `Male_liver_15wk_MS316_G221_M69`, `Male_liver_15wk_MS316_G221_M70`, `Male_liver_15wk_MS316_G221_M71`, `Male_liver_15wk_MS316_G221_M72`, `Male_liver_15wk_MS316_G221_M73`, `Male_liver_15wk_MS316_G221_M74` 
6: Unknown columns: `Male_liver_8wk_G216_G216_M61`, `Male_liver_8wk_G216_G216_M62`, `Male_liver_8wk_G216_G216_M63`, `Male_liver_8wk_G216_G216_M64`, `Male_liver_8wk_G216_G216_M65`, `Male_liver_8wk_G216_G216_M66` 
Creating Volcano plots
+ Rscript volcano_plots.R --segex_files_path ./output/Segex_09d/Segex09d_ExonCollapsed --sample_labels ../00_Setup_Pipeline/Sample_Labels.txt --comparisons ../00_Setup_Pipeline/Comparisons.txt --output_prefix ./output/alldots_Segex09d_ExonCollapsed
Loading required package: argparser
[[1]]
[1] FALSE

$help
[1] FALSE

$opts
[1] NA

$segex_files_path
[1] "./output/Segex_09d/Segex09d_ExonCollapsed"

$sample_labels
[1] "../00_Setup_Pipeline/Sample_Labels.txt"

$comparisons
[1] "../00_Setup_Pipeline/Comparisons.txt"

$output_prefix
[1] "./output/alldots_Segex09d_ExonCollapsed"

$nonsignif_fraction
[1] 1

Loading required package: usethis
Skipping install of 'NotationConverter' from a local remote, the SHA1 (0.0.0.90) has not changed since last install.
  Use `force = TRUE` to force installation
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.4.1     ✔ purrr   1.0.1
✔ tibble  3.1.7     ✔ dplyr   1.1.0
✔ tidyr   1.3.0     ✔ stringr 1.5.0
✔ readr   2.1.2     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Attaching package: ‘gridExtra’

The following object is masked from ‘package:dplyr’:

    combine


Attaching package: ‘patchwork’

The following object is masked from ‘package:cowplot’:

    align_plots

Rows: 3 Columns: 3
── Column specification ────────────────────────────────────────────────────────
Delimiter: ";"
chr (2): Condition_1, Condition_2
dbl (1): Comparison_Number

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 24 Columns: 5
── Column specification ────────────────────────────────────────────────────────
Delimiter: ";"
chr (5): Group, Condition_Name, Sample_ID, Description, Color

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
[1] "Saving individual scale plots..."
   user  system elapsed 
  8.335   0.238   8.632 
Warning messages:
1: Removed 75212 rows containing missing values (`geom_text_repel()`). 
2: Removed 75688 rows containing missing values (`geom_text_repel()`). 
3: Removed 75696 rows containing missing values (`geom_text_repel()`). 
4: ggrepel: 475 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
5: ggrepel: 10 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
6: ggrepel: 33 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
[1] "Saving common scale plots..."
   user  system elapsed 
  6.627   0.087   6.736 
Warning messages:
1: Removed 75212 rows containing missing values (`geom_text_repel()`). 
2: Removed 75688 rows containing missing values (`geom_text_repel()`). 
3: Removed 75696 rows containing missing values (`geom_text_repel()`). 
4: ggrepel: 489 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
5: ggrepel: 89 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
6: ggrepel: 88 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
+ Rscript volcano_plots.R --segex_files_path ./output/Segex_09d/Segex09d_ExonCollapsed --sample_labels ../00_Setup_Pipeline/Sample_Labels.txt --comparisons ../00_Setup_Pipeline/Comparisons.txt --nonsignif_fraction 0.1 --output_prefix ./output/10percent_Segex09d_ExonCollapsed
Loading required package: argparser
[[1]]
[1] FALSE

$help
[1] FALSE

$opts
[1] NA

$segex_files_path
[1] "./output/Segex_09d/Segex09d_ExonCollapsed"

$sample_labels
[1] "../00_Setup_Pipeline/Sample_Labels.txt"

$comparisons
[1] "../00_Setup_Pipeline/Comparisons.txt"

$output_prefix
[1] "./output/10percent_Segex09d_ExonCollapsed"

$nonsignif_fraction
[1] 0.1

Loading required package: usethis
Skipping install of 'NotationConverter' from a local remote, the SHA1 (0.0.0.90) has not changed since last install.
  Use `force = TRUE` to force installation
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.4.1     ✔ purrr   1.0.1
✔ tibble  3.1.7     ✔ dplyr   1.1.0
✔ tidyr   1.3.0     ✔ stringr 1.5.0
✔ readr   2.1.2     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Attaching package: ‘gridExtra’

The following object is masked from ‘package:dplyr’:

    combine


Attaching package: ‘patchwork’

The following object is masked from ‘package:cowplot’:

    align_plots

Rows: 3 Columns: 3
── Column specification ────────────────────────────────────────────────────────
Delimiter: ";"
chr (2): Condition_1, Condition_2
dbl (1): Comparison_Number

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 24 Columns: 5
── Column specification ────────────────────────────────────────────────────────
Delimiter: ";"
chr (5): Group, Condition_Name, Sample_ID, Description, Color

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
[1] "Saving individual scale plots..."
   user  system elapsed 
  4.818   0.089   4.947 
Warning messages:
1: Removed 7522 rows containing missing values (`geom_text_repel()`). 
2: Removed 7569 rows containing missing values (`geom_text_repel()`). 
3: Removed 7570 rows containing missing values (`geom_text_repel()`). 
4: ggrepel: 475 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
5: ggrepel: 7 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
6: ggrepel: 21 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
[1] "Saving common scale plots..."
   user  system elapsed 
  3.075   0.020   3.106 
Warning messages:
1: Removed 7522 rows containing missing values (`geom_text_repel()`). 
2: Removed 7569 rows containing missing values (`geom_text_repel()`). 
3: Removed 7570 rows containing missing values (`geom_text_repel()`). 
4: ggrepel: 489 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
5: ggrepel: 89 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
6: ggrepel: 88 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
All files copied. Done 
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
mpyatkov running 0 jobs
Periodically checking until jobs complete (please wait)...
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts/14_final_summary /projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
WARNING: logs directory does not exist. Analysis of logs will not be produced
Done: Step_14_G221_RNASEQ_MS316

 -------------------------
/projectnb/wax-dk/max/G221_RNASEQ_MS316/Scripts
END: 14

 -------------------------Pipeline is done, check out your results!
==========================================================
Finished on : Mon Feb 26 16:23:18 EST 2024
0 hours, 31 minutes and 20 seconds elapsed.
