Thanks Alex, I tried that. still got the same error. Please see my attached log...thanks
WARNING: long repeat for junction # 408931 : chr16 21414159 21414284; left shift = 4; right shift = 255
Jan 30 17:14:17 Finished preparing junctions
Jan 30 17:14:17 ..... inserting junctions into the genome indices
Jan 30 17:14:18 Finished SA search: number of new junctions=750, old junctions=253315
Jan 30 17:14:18 Finished sorting SA indicesL nInd=267000
Jan 30 17:15:41 Finished inserting junction indices
Jan 30 17:15:46 Finished SAi
Jan 30 17:15:46 ..... finished inserting junctions into genome
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread0 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread1 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread2 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread3 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread4 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread4 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread5 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread5 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread6 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread6 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread7 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread7 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread8 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread8 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread9 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread9 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread10 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread10 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread11 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread11 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread12 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread12 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread13 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread13 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread14 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread14 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread15 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread15 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread16 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread16 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread17 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread17 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread18 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread18 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread19 ... ok
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate2.thread19 ... ok
Created thread # 1
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Thread #8 end of input stream, nextChar=-1
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Jan 30 17:20:36 Loaded database junctions from the 1st pass file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARpass1//SJ.out.tab: 462866 total junctions
WARNING: long repeat for junction # 92012 : chr7 1195831 1195893; left shift = 34; right shift = 255
WARNING: long repeat for junction # 108773 : chr8 86759769 86765941; left shift = 1; right shift = 255
WARNING: long repeat for junction # 159518 : chr12 125396597 125396824; left shift = 93; right shift = 255
WARNING: long repeat for junction # 190342 : chr16 21846536 21847304; left shift = 30; right shift = 255
WARNING: long repeat for junction # 344643 : chr8 86759769 86765941; left shift = 1; right shift = 255
WARNING: long repeat for junction # 408931 : chr16 21414159 21414284; left shift = 4; right shift = 255
Jan 30 17:20:46 Finished preparing junctions
Jan 30 17:20:46 ..... inserting junctions into the genome indices
Jan 30 17:20:47 Finished SA search: number of new junctions=115, old junctions=254065
Jan 30 17:20:48 Finished sorting SA indicesL nInd=40940
Jan 30 17:22:11 Finished inserting junction indices
Jan 30 17:22:16 Finished SAi
Jan 30 17:22:17 ..... finished inserting junctions into genome
Opening the file: /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread0 ... failed!
EXITING because of FATAL ERROR: could not create output file /media/NGS_21NOV/test_data/CS412006_S1/pipeline_output/CS412006_S1__STARtmp//FilterBySJoutFiles.mate1.thread0