EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree with the ac

[kevin.pan]

Hi,

I keep running into this error message no matter how I set the --runThreadN (I tried 8,6,4). I also tried different combination with --limitBAMsortRAM (0,30000000000,40000000000). 

I was using SGE system submitting jobs -pe shared N (N is always kept same as --runThreadN).

Now I totally follow GDC TCGA mRNA pipeline using STAR 2.4.2. (TCGA pipeline https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#mrna-expression-workflow)

Could you provide some suggestions on what parameters I should use?  Thanks!!!

And here are my commands:

STAR --genomeDir $GenomeDir --readFilesIn $readsFiles_split --runThreadN 8 --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --alignIntronMax 500000 --alignMatesGapMax 1000000 --sjdbScore 2 --alignSJDBoverhangMin 1 --genomeLoad NoSharedMemory --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --sjdbOverhang 99 --outSAMstrandField intronMotif --outSAMtype None --outSAMmode None --readFilesCommand zcat --outFileNamePrefix ${OutDir}/

STAR --runMode genomeGenerate --genomeDir "$OutDir".genome --genomeFastaFiles $GenomeFasta --sjdbOverhang 99 --runThreadN 8 --sjdbFileChrStartEnd ${OutDir}/SJ.out.tab

STAR --genomeDir "$OutDir".genome --readFilesIn $readsFiles_split --runThreadN 8 --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --alignIntronMax 500000 --alignMatesGapMax 1000000 --sjdbScore 2 --alignSJDBoverhangMin 1 --genomeLoad NoSharedMemory --limitBAMsortRAM 0 --readFilesCommand zcat --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --sjdbOverhang 99 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN:1.4 --outFileNamePrefix ${OutDir}/

Error message:

EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree with the actual size on disk: 61183420   19194135   8

[Alexander Dobin]

Hi Kevin,

this problem may be caused by insufficient disk space on ${OutDir}, please check this out.

Also, please try a later version of STAR, preferably the latest 2.5.3a?

2.4.2 is pretty old and the problem might have been fixed in the later releases.

Cheers

Alex

[Chen Mordechay]

Hi Alex!

I'm actually experiencing the same issue with STAR 2.5.3a.
Any ideas on how to go about resolving this issue?

Best,
Chen

[Alexander Dobin]

Hi Chen,

have you checked that you have sufficient disk space?

Please send me the Log.out file.

Cheers

Alex

[djk...@gmail.com]

Hi Alex,

I am also experiencing this error and I have confirmed that I have room on /tmp (7.0T). The numbers reported in the error include a conspicuous 0 though. Any thoughts?

==> D0P1.err <==

EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree with the actual size on disk: 740987939   0   16

Aug 29 22:10:20 ...... FATAL ERROR, exiting

==> D0P1.out <==

Aug 29 18:34:15 ..... Started STAR run

Aug 29 18:34:15 ..... Loading genome

Aug 29 18:34:18 ..... Started mapping

Aug 29 22:10:18 ..... Started sorting BAM

Thanks in advance for the help and for the amazing software!

David

[Alexander Dobin]

Hi David.

STAR uses the run directory for the temporary storage (_STARtmp/), so you would need to check the empty disk space there.

If there is enough space, please try to re-run after deleting everything in the run directory.

If the problem persists, please send me the Log.out file and the output of 

$ ls -lth _STARtmp/

Cheers

Alex

[djk...@gmail.com]

Hi Alex,

I tried running in a fresh directory to no avail. Here is the listing of the _STARtmp,

-rwxrwx---  1 konkind konkind 44M Aug 30 18:37 Unmapped.out.mate2.thread33
-rwxrwx---  1 konkind konkind 44M Aug 30 18:37 Unmapped.out.mate1.thread33
-rwxrwx---  1 konkind konkind 44M Aug 30 18:37 Unmapped.out.mate2.thread9
-rwxrwx---  1 konkind konkind 44M Aug 30 18:37 Unmapped.out.mate1.thread9
-rwxrwx---  1 konkind konkind 45M Aug 30 18:37 Unmapped.out.mate2.thread5
-rwxrwx---  1 konkind konkind 45M Aug 30 18:37 Unmapped.out.mate1.thread5
-rwxrwx---  1 konkind konkind 37M Aug 30 18:36 Unmapped.out.mate2.thread37
-rwxrwx---  1 konkind konkind 38M Aug 30 18:36 Unmapped.out.mate1.thread37
-rwxrwx---  1 konkind konkind 44M Aug 30 18:36 Unmapped.out.mate2.thread31
-rwxrwx---  1 konkind konkind 44M Aug 30 18:36 Unmapped.out.mate1.thread31
-rwxrwx---  1 konkind konkind 43M Aug 30 18:36 Unmapped.out.mate2.thread45
-rwxrwx---  1 konkind konkind 43M Aug 30 18:36 Unmapped.out.mate1.thread45
-rwxrwx---  1 konkind konkind 46M Aug 30 18:35 Unmapped.out.mate2.thread44
-rwxrwx---  1 konkind konkind 46M Aug 30 18:35 Unmapped.out.mate1.thread44
-rwxrwx---  1 konkind konkind 43M Aug 30 18:35 Unmapped.out.mate2.thread38
-rwxrwx---  1 konkind konkind 44M Aug 30 18:35 Unmapped.out.mate1.thread38
-rwxrwx---  1 konkind konkind 37M Aug 30 18:35 Unmapped.out.mate2.thread41
-rwxrwx---  1 konkind konkind 37M Aug 30 18:35 Unmapped.out.mate1.thread41
-rwxrwx---  1 konkind konkind 38M Aug 30 18:35 Unmapped.out.mate2.thread28
-rwxrwx---  1 konkind konkind 38M Aug 30 18:35 Unmapped.out.mate1.thread28
-rwxrwx---  1 konkind konkind 44M Aug 30 18:34 Unmapped.out.mate2.thread1
-rwxrwx---  1 konkind konkind 44M Aug 30 18:34 Unmapped.out.mate1.thread1
-rwxrwx---  1 konkind konkind 46M Aug 30 18:34 Unmapped.out.mate2.thread35
-rwxrwx---  1 konkind konkind 46M Aug 30 18:34 Unmapped.out.mate1.thread35
-rwxrwx---  1 konkind konkind 39M Aug 30 18:34 Unmapped.out.mate2.thread42
-rwxrwx---  1 konkind konkind 41M Aug 30 18:34 Unmapped.out.mate2.thread30
-rwxrwx---  1 konkind konkind 40M Aug 30 18:34 Unmapped.out.mate1.thread42
-rwxrwx---  1 konkind konkind 41M Aug 30 18:34 Unmapped.out.mate1.thread30
-rwxrwx---  1 konkind konkind 37M Aug 30 18:33 Unmapped.out.mate2.thread27
-rwxrwx---  1 konkind konkind 37M Aug 30 18:33 Unmapped.out.mate1.thread27
-rwxrwx---  1 konkind konkind 44M Aug 30 18:33 Unmapped.out.mate2.thread29
-rwxrwx---  1 konkind konkind 44M Aug 30 18:33 Unmapped.out.mate1.thread29
-rwxrwx---  1 konkind konkind 38M Aug 30 18:33 Unmapped.out.mate2.thread43
-rwxrwx---  1 konkind konkind 38M Aug 30 18:33 Unmapped.out.mate1.thread43
-rwxrwx---  1 konkind konkind 38M Aug 30 18:33 Unmapped.out.mate2.thread18
-rwxrwx---  1 konkind konkind 39M Aug 30 18:33 Unmapped.out.mate1.thread18
-rwxrwx---  1 konkind konkind 37M Aug 30 18:33 Unmapped.out.mate2.thread15
-rwxrwx---  1 konkind konkind 37M Aug 30 18:33 Unmapped.out.mate1.thread15
-rwxrwx---  1 konkind konkind 37M Aug 30 18:31 Unmapped.out.mate2.thread12
-rwxrwx---  1 konkind konkind 37M Aug 30 18:31 Unmapped.out.mate1.thread12
-rwxrwx---  1 konkind konkind 37M Aug 30 18:31 Unmapped.out.mate2.thread7
-rwxrwx---  1 konkind konkind 37M Aug 30 18:31 Unmapped.out.mate1.thread7
-rwxrwx---  1 konkind konkind 40M Aug 30 18:31 Unmapped.out.mate2.thread23
-rwxrwx---  1 konkind konkind 40M Aug 30 18:31 Unmapped.out.mate1.thread23
-rwxrwx---  1 konkind konkind 37M Aug 30 18:31 Unmapped.out.mate2.thread19
-rwxrwx---  1 konkind konkind 37M Aug 30 18:31 Unmapped.out.mate1.thread19
-rwxrwx---  1 konkind konkind 38M Aug 30 18:31 Unmapped.out.mate2.thread11
-rwxrwx---  1 konkind konkind 38M Aug 30 18:31 Unmapped.out.mate1.thread11
-rwxrwx---  1 konkind konkind 37M Aug 30 18:29 Unmapped.out.mate2.thread10
-rwxrwx---  1 konkind konkind 37M Aug 30 18:29 Unmapped.out.mate1.thread10
-rwxrwx---  1 konkind konkind 44M Aug 30 18:29 Unmapped.out.mate2.thread24
-rwxrwx---  1 konkind konkind 45M Aug 30 18:29 Unmapped.out.mate1.thread24
-rwxrwx---  1 konkind konkind 37M Aug 30 18:29 Unmapped.out.mate2.thread6
-rwxrwx---  1 konkind konkind 37M Aug 30 18:29 Unmapped.out.mate1.thread6
-rwxrwx---  1 konkind konkind 37M Aug 30 18:28 Unmapped.out.mate2.thread0
-rwxrwx---  1 konkind konkind 37M Aug 30 18:28 Unmapped.out.mate1.thread0
-rwxrwx---  1 konkind konkind 38M Aug 30 18:27 Unmapped.out.mate2.thread32
-rwxrwx---  1 konkind konkind 38M Aug 30 18:27 Unmapped.out.mate1.thread32
-rwxrwx---  1 konkind konkind 43M Aug 30 18:27 Unmapped.out.mate2.thread26
-rwxrwx---  1 konkind konkind 44M Aug 30 18:27 Unmapped.out.mate1.thread26
-rwxrwx---  1 konkind konkind 42M Aug 30 18:27 Unmapped.out.mate2.thread34
-rwxrwx---  1 konkind konkind 42M Aug 30 18:27 Unmapped.out.mate1.thread34
-rwxrwx---  1 konkind konkind 38M Aug 30 18:26 Unmapped.out.mate2.thread22
-rwxrwx---  1 konkind konkind 38M Aug 30 18:26 Unmapped.out.mate1.thread22
-rwxrwx---  1 konkind konkind 37M Aug 30 18:25 Unmapped.out.mate2.thread17
-rwxrwx---  1 konkind konkind 37M Aug 30 18:25 Unmapped.out.mate1.thread17
-rwxrwx---  1 konkind konkind 37M Aug 30 18:23 Unmapped.out.mate2.thread39
-rwxrwx---  1 konkind konkind 37M Aug 30 18:23 Unmapped.out.mate1.thread39
-rwxrwx---  1 konkind konkind 37M Aug 30 18:20 Unmapped.out.mate2.thread21
-rwxrwx---  1 konkind konkind 38M Aug 30 18:20 Unmapped.out.mate1.thread21
-rwxrwx---  1 konkind konkind 37M Aug 30 18:18 Unmapped.out.mate2.thread36
-rwxrwx---  1 konkind konkind 37M Aug 30 18:18 Unmapped.out.mate1.thread36
-rwxrwx---  1 konkind konkind 37M Aug 30 18:17 Unmapped.out.mate2.thread40
-rwxrwx---  1 konkind konkind 37M Aug 30 18:17 Unmapped.out.mate1.thread40
-rwxrwx---  1 konkind konkind 37M Aug 30 18:15 Unmapped.out.mate2.thread25
-rwxrwx---  1 konkind konkind 37M Aug 30 18:15 Unmapped.out.mate1.thread25
-rwxrwx---  1 konkind konkind 37M Aug 30 18:14 Unmapped.out.mate2.thread8
-rwxrwx---  1 konkind konkind 37M Aug 30 18:14 Unmapped.out.mate1.thread8
-rwxrwx---  1 konkind konkind 44M Aug 30 18:12 Unmapped.out.mate2.thread13
-rwxrwx---  1 konkind konkind 44M Aug 30 18:12 Unmapped.out.mate1.thread13
-rwxrwx---  1 konkind konkind 37M Aug 30 18:11 Unmapped.out.mate2.thread14
-rwxrwx---  1 konkind konkind 37M Aug 30 18:11 Unmapped.out.mate1.thread14
-rwxrwx---  1 konkind konkind 38M Aug 30 18:09 Unmapped.out.mate2.thread2
-rwxrwx---  1 konkind konkind 38M Aug 30 18:09 Unmapped.out.mate1.thread2
-rwxrwx---  1 konkind konkind 37M Aug 30 18:08 Unmapped.out.mate2.thread4
-rwxrwx---  1 konkind konkind 37M Aug 30 18:07 Unmapped.out.mate1.thread4
-rwxrwx---  1 konkind konkind 38M Aug 30 18:03 Unmapped.out.mate2.thread16
-rwxrwx---  1 konkind konkind 38M Aug 30 18:03 Unmapped.out.mate1.thread16
-rwxrwx---  1 konkind konkind 37M Aug 30 17:59 Unmapped.out.mate2.thread3
-rwxrwx---  1 konkind konkind 38M Aug 30 17:59 Unmapped.out.mate1.thread3
-rwxrwx---  1 konkind konkind 39M Aug 30 17:52 Unmapped.out.mate2.thread20
-rwxrwx---  1 konkind konkind 39M Aug 30 17:52 Unmapped.out.mate1.thread20
-rwxrwx---  1 konkind konkind 58M Aug 30 17:11 FilterBySJoutFiles.mate2.thread42
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate2.thread8
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate2.thread24
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread12
-rwxrwx---  1 konkind konkind 58M Aug 30 17:11 FilterBySJoutFiles.mate2.thread30
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread11
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread28
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate2.thread45
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate2.thread38
-rwxrwx---  1 konkind konkind 68M Aug 30 17:11 FilterBySJoutFiles.mate2.thread35
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread18
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread22
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate2.thread26
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate2.thread31
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread17
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate2.thread13
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate2.thread19
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread27
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate2.thread0
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread15
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate2.thread41
-rwxrwx---  1 konkind konkind 57M Aug 30 17:11 FilterBySJoutFiles.mate2.thread34
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread37
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread36
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread25
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread32
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate2.thread33
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread10
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread43
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread21
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate2.thread40
-rwxrwx---  1 konkind konkind 58M Aug 30 17:11 FilterBySJoutFiles.mate2.thread23
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate2.thread29
-rwxrwx---  1 konkind konkind 68M Aug 30 17:11 FilterBySJoutFiles.mate2.thread44
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate2.thread39
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread20
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread16
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread14
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate2.thread9
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread7
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate2.thread5
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread4
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread2
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread3
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate2.thread1
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate2.thread6
-rwxrwx---  1 konkind konkind 58M Aug 30 17:11 FilterBySJoutFiles.mate1.thread30
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread28
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate1.thread29
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate1.thread24
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread27
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate1.thread26
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate1.thread45
-rwxrwx---  1 konkind konkind 58M Aug 30 17:11 FilterBySJoutFiles.mate1.thread23
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread25
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread22
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread21
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread43
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread41
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread39
-rwxrwx---  1 konkind konkind 68M Aug 30 17:11 FilterBySJoutFiles.mate1.thread44
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread0
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread37
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread20
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread19
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread36
-rwxrwx---  1 konkind konkind 58M Aug 30 17:11 FilterBySJoutFiles.mate1.thread42
-rwxrwx---  1 konkind konkind 68M Aug 30 17:11 FilterBySJoutFiles.mate1.thread35
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread18
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate1.thread38
-rwxrwx---  1 konkind konkind 58M Aug 30 17:11 FilterBySJoutFiles.mate1.thread34
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate1.thread33
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread17
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread32
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread15
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate1.thread31
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread40
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread16
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread14
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread12
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate1.thread13
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread10
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread11
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread8
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate1.thread9
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread7
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate1.thread5
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread6
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread4
-rwxrwx---  1 konkind konkind 60M Aug 30 17:11 FilterBySJoutFiles.mate1.thread3
-rwxrwx---  1 konkind konkind 59M Aug 30 17:11 FilterBySJoutFiles.mate1.thread2
-rwxrwx---  1 konkind konkind 69M Aug 30 17:11 FilterBySJoutFiles.mate1.thread1
drwxrwx--- 48 konkind konkind 910 Aug 30 12:50 BAMsort
-rwxrwx---  1 konkind konkind 122 Aug 30 12:36 readsCommand_read2
-rwxrwx---  1 konkind konkind  96 Aug 30 12:36 readFilesIn.info
prwxrwx---  1 konkind konkind   0 Aug 30 12:36 tmp.fifo.read2
-rwxrwx---  1 konkind konkind 122 Aug 30 12:36 readsCommand_read1
prwxrwx---  1 konkind konkind   0 Aug 30 12:36 tmp.fifo.read1

Thank you,

David

[Alexander Dobin]

Hi David,

what is the output of 

$ df .

and

$ ls -lh _STARtmp/BAMsort/

Thanks!

Alex

[djk...@gmail.com]

Hi Alex,

Plenty of room...

 $ df . -h
Filesystem         Size  Used Avail Use% Mounted on
vacuole:/ifs/data  1.5P  840T  661T  56% /storage

 $ ls -h BAMsort/
0  1  10  11  12  13  14  15  16  17  18  19  2  20  21  22  23  24  25  26  27  28  29  3  30  31  32  33  34  35  36  37  38  39  4  40  41  42  43  44  45  5  6  7  8  9

example of the contents of dir 1 in BAMsort:

$ls -lhtr 1
total 286M
-rwxrwx--- 1 konkind konkind   0 Aug 30 12:50 17
-rwxrwx--- 1 konkind konkind   0 Aug 30 17:11 17.BySJout
-rwxrwx--- 1 konkind konkind 16M Aug 30 18:34 0
-rwxrwx--- 1 konkind konkind 18M Aug 30 18:34 1
-rwxrwx--- 1 konkind konkind 21M Aug 30 18:34 2
-rwxrwx--- 1 konkind konkind 20M Aug 30 18:34 3
-rwxrwx--- 1 konkind konkind 21M Aug 30 18:34 4
-rwxrwx--- 1 konkind konkind 20M Aug 30 18:34 5
-rwxrwx--- 1 konkind konkind 21M Aug 30 18:34 6
-rwxrwx--- 1 konkind konkind 20M Aug 30 18:34 7
-rwxrwx--- 1 konkind konkind 21M Aug 30 18:34 8
-rwxrwx--- 1 konkind konkind 20M Aug 30 18:34 9
-rwxrwx--- 1 konkind konkind 20M Aug 30 18:34 10

Thanks for the assistance,

David

[Alexander Dobin]

Hi David,

I cannot make sense of the contents of BAMsort/ . Please send me the Log.out file.

Cheers

Alex

[djk...@gmail.com]

Hi Alex,

I had to upload it to Google drive, you can get it at:

https://drive.google.com/file/d/0B7DPtPzkKX_pcW16cjR6QkdtS0k/view?usp=sharing

Thanks again,

David

[Alexander Dobin]

Hi David,

you are using a pretty old version 2.4.2a - please try the latest one https://github.com/alexdobin/STAR/releases/tag/2.5.3a, as many bugs have been fixed.

Please re-generate the genome with the new version - I would recommend using --genomeChrBinNbits 11 to reduce RAM consumption for a genome with the large number of contigs. Also, you may want to consider merging the small contigs into one super-contig - this will increase the mapping speed greatly - please check this post: https://groups.google.com/d/msg/rna-star/G8mv5t5EWR0/tXyrE-jUAQAJ .

Cheers

Alex