Solution: check that you have permission to write this file

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Jack Yen

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Jan 23, 2018, 3:26:07 PM1/23/18

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Hi,

I keep getting this error message that I couldn't figure out why. I tried run it as root but still the same.

any suggestion would be very helpful. Thanks

this is my command

"STAR --runThreadN 20 --genomeDir /home/lee/reference/hg19/starindex --outFileNamePrefix /media/NGS_21NOV/test_data/CTL1_S1_L001/downsample/pipeline_output/CTL1_S1_ --outSAMattrRGline ID:1 "SM:CTL1_S1_" --outSAMattributes NH NM MD --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMmapqUnique 50 --readFilesCommand zcat --readFilesIn /media/NGS_21NOV/test_data/CTL1_S1_L001/downsample/sample1_p1.fastq.gz /media/NGS_21NOV/test_data/CTL1_S1_L001/downsample/sample1_p2.fastq.gz --sjdbGTFfile "/media/fs02/reference/hg19/annotation/genes.gtf" --outFilterType BySJout --outSJfilterCountUniqueMin -1 2 2 2 --outSJfilterCountTotalMin -1 2 2 2 --outFilterIntronMotifs RemoveNoncanonical --twopassMode Basic

this is the error
EXITING because of FATAL ERROR: could not create output file /media/NGS_21NOV/test_data/CTL1_S1_L001/downsample/pipeline_output/CTL1_S1__STARtmp//FilterBySJoutFiles.mate1.thread0

Solution: check that you have permission to write this file

Jan 23 15:20:34 ...... FATAL ERROR, exiting

Alexander Dobin

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Jan 24, 2018, 11:23:00 AM1/24/18

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Hi Jack,

please try to increase the number of allowed open files

$ ulimit -n 10000

Cheers

Alex

Jack Yen

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Jan 31, 2018, 10:02:18 AM1/31/18

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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

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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

Solution: check that you have permission to write this file

Jan 30 17:23:49 ...... FATAL ERROR, exiting

Alexander Dobin

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Feb 5, 2018, 12:22:23 PM2/5/18

to rna-star

Hi Jack,

the "/media" filesystem, is it standard Linux partition? If not, it may create some problems.

Please try to run it with mostly default parameters, i.e.
STAR --genomeDir /home/lee/reference/hg19/starindex --outFileNamePrefix /media/NGS_21NOV/test_data/CTL1_S1_L001/downsample/pipeline_output/CTL1_S1_ --readFilesCommand zcat --readFilesIn /media/NGS_21NOV/test_data/CTL1_S1_L001/downsample/sample1_p1.fastq.gz /media/NGS_21NOV/test_data/CTL1_S1_L001/downsample/sample1_p2.fastq.gz

Cheers