Error at end of STAR run: double free or corruption (fasttop)

Tom Harrop

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Jan 7, 2016, 10:53:05 AM1/7/16

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Hi Alex,

I've updated to STAR_2.5.0c on a new installation of Ubuntu 15.10, and I'm getting an error at the end of my runs.

Jan 07 15:49:24 ..... Started STAR run
Jan 07 15:49:24 ..... Loading genome
Jan 07 15:49:24 ..... Started mapping
Jan 07 16:08:13 ..... Finished successfully
*** Error in `/usr/local/bin/STAR': double free or corruption (fasttop): 0x00000000008592d0 ***

It looks to me like the mapping completed. Both Log.out and Log.progress.out finish with "ALL DONE!".

Here are my command-line parameters:

/usr/local/bin/STAR --runThreadN 4 --genomeDir path/to/index --outSJfilterReads Unique \
    --readFilesCommand zcat --outSAMtype None --readFilesIn read1.fastq.gz read2.fastq.gz \
    --outFileNamePrefix path/to/output/ --genomeLoad LoadAndKeep

Sorry for the lack of information but I'm not sure what you need for this error. If you let me know I will attach it.

Thanks,

Tom

Alexander Dobin

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Jan 7, 2016, 12:44:35 PM1/7/16

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Hi Tom,

did you try to run this example with an earlier version of STAR (which one?), and it did not give the same error?

Could you please try to run the pre-compiled STAR executables?

Cheers

Alex

Tom Harrop

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Jan 8, 2016, 4:43:26 AM1/8/16

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Switching to the pre-compiled static binary worked. Should've tried that before posting. Thanks.

Tom Harrop

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Jan 8, 2016, 4:43:31 AM1/8/16

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Tom Harrop

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Feb 19, 2016, 7:18:00 AM2/19/16

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Hi Alex,

Sorry to reopen this, but it's just popped up again with the pre-compiled 2.5.1b binary.

The mapping seems to finish successfully. Is this a problem with my system? I'm not sure how to troubleshoot, but I'm attaching a Log.out file and pasting below the standard error/output from a run I did using the static binary.

Thanks,

Tom

Feb 19 11:21:36 ..... Started STAR run
Feb 19 11:21:38 ..... Loading genome
Feb 19 11:22:03 ..... Started mapping
Feb 19 11:27:01 ..... Started sorting BAM
Feb 19 11:28:23 ..... Finished successfully
*** glibc detected *** /usr/local/bin/STAR: double free or corruption (fasttop): 0x00000000018c3b00 ***
======= Backtrace: =========
[0x5bcbe2]
[0x5bf648]
[0x40b870]
[0x590a2b]
[0x400509]
======= Memory map: ========
00400000-006c1000 r-xp 00000000 08:22 11152075                           /usr/local/bin/STAR
008c1000-008d2000 rw-p 002c1000 08:22 11152075                           /usr/local/bin/STAR
008d2000-008dc000 rw-p 00000000 00:00 0 
0189f000-0f785000 rw-p 00000000 00:00 0                                  [heap]
7f6f1bf41000-7f6f24000000 rw-p 00000000 00:00 0 
7f6f24000000-7f6f259ba000 rw-p 00000000 00:00 0 
7f6f259ba000-7f6f28000000 ---p 00000000 00:00 0 
7f6f2c000000-7f6f2d9ba000 rw-p 00000000 00:00 0 
7f6f2d9ba000-7f6f30000000 ---p 00000000 00:00 0 
7f6f30000000-7f6f319ba000 rw-p 00000000 00:00 0 
7f6f319ba000-7f6f34000000 ---p 00000000 00:00 0 
7f6f34000000-7f6f359ba000 rw-p 00000000 00:00 0 
7f6f359ba000-7f6f38000000 ---p 00000000 00:00 0 
7f6f38000000-7f6f399ba000 rw-p 00000000 00:00 0 
7f6f399ba000-7f6f3c000000 ---p 00000000 00:00 0 
7f6f3c000000-7f6f3d9ba000 rw-p 00000000 00:00 0 
7f6f3d9ba000-7f6f40000000 ---p 00000000 00:00 0 
7f6f43e64000-7f6f43e65000 ---p 00000000 00:00 0 
7f6f43e65000-7f6f44665000 rw-p 00000000 00:00 0                          [stack:4150]
7f6f44665000-7f6f44666000 ---p 00000000 00:00 0 
7f6f44666000-7f6f44e66000 rw-p 00000000 00:00 0                          [stack:4151]
7f6f44e66000-7f6f44e67000 ---p 00000000 00:00 0 
7f6f44e67000-7f6f45667000 rw-p 00000000 00:00 0                          [stack:4152]
7f6f45667000-7f6f45668000 ---p 00000000 00:00 0 
7f6f45668000-7f6f45e68000 rw-p 00000000 00:00 0                          [stack:4153]
7f6f46669000-7f6f4666a000 ---p 00000000 00:00 0 
7f6f4666a000-7f6f8c05f000 rw-p 00000000 00:00 0                          [stack:4154]
7f7038e74000-7f7038e75000 rw-p 00000000 00:00 0 
7f7038e75000-7f7038e76000 rw-s 00000000 00:05 1703943                    /SYSV1701044d (deleted)
7f7038e76000-7f7038e77000 rw-p 00000000 00:00 0 
7ffdccdfa000-7ffdcce2b000 rw-p 00000000 00:00 0                          [stack]
7ffdccee6000-7ffdccee8000 r--p 00000000 00:00 0                          [vvar]
7ffdccee8000-7ffdcceea000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

uvPAR.2.Log.out

Alexander Dobin

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Feb 19, 2016, 3:50:44 PM2/19/16

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Hi Tom,

have you tried all variants with 2.5.1b: static/dynamic/compiled-yourself?

This problem is happening after STAR finished all calculations, so it does not affect the results - but it's annoying.

I cannot reproduce it on my system unfortunately, and valgrind does not point to any errors...

Cheers

Alex

...

Tom Harrop

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Feb 22, 2016, 5:55:57 PM2/22/16

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Hi Alex,

The only real effect is that my scripts aren't exiting cleanly, so while it's annoying it's not the end of the world.

Yes, I had the same problem with the static, dynamic and self-compiled flavours of 2.5.1b.

Today I compiled STAR from your Github repo (2.5.1b_modified). With that binary I successfully mapped 48 libraries, including ones that were failing last week. After that, the next 8 libraries failed (these ones had mapped succesfully last week). It seems like the problem is not reproducible. I'm going to look into potential (hardware/software) issues with my system, but I'll post again if the problem goes away or I find a repeatable example.

Thanks for the help,

Tom

rspreafico

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Feb 23, 2016, 11:39:03 AM2/23/16

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Hi

I run into the same issue. This is the first time I see it. Older versions of STAR never game me issues of this kind. I am running the static version, as I have always been doing with older versions too. I am running Ubuntu 15.10.

Here is my command, as well as the error:

STAR --genomeDir /opt/ngs_indexes/star/mm10.primary_assembly.gencode.vM6_refchrom.50bp --runThreadN 4 --genomeLoad LoadAndKeep --readFilesIn read1.fastq read2.fastq --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 17179869184 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --seedSearchStartLmax 30

*** glibc detected *** STAR: double free or corruption (fasttop): 0x000000000186aec0 ***

======= Backtrace: =========

[0x5bcbe2]

[0x5bf648]

[0x40b870]

[0x590a2b]

[0x400509]

======= Memory map: ========

00400000-006c1000 r-xp 00000000 fc:01 9452672 /opt/STAR-2.5.1b/bin/Linux_x86_64_static/STAR

008c1000-008d2000 rw-p 002c1000 fc:01 9452672 /opt/STAR-2.5.1b/bin/Linux_x86_64_static/STAR

008d2000-008dc000 rw-p 00000000 00:00 0

01846000-0f0bb000 rw-p 00000000 00:00 0 [heap]

7f47f3e82000-7f4804000000 rw-p 00000000 00:00 0

7f4804000000-7f4804fd1000 rw-p 00000000 00:00 0

7f4804fd1000-7f4808000000 ---p 00000000 00:00 0

7f480c000000-7f480cfd2000 rw-p 00000000 00:00 0

7f480cfd2000-7f4810000000 ---p 00000000 00:00 0

7f4810000000-7f48100ee000 rw-p 00000000 00:00 0

7f48100ee000-7f4814000000 ---p 00000000 00:00 0

7f4814000000-7f4814f77000 rw-p 00000000 00:00 0

7f4814f77000-7f4818000000 ---p 00000000 00:00 0

7f4818000000-7f4818f92000 rw-p 00000000 00:00 0

7f4818f92000-7f481c000000 ---p 00000000 00:00 0

7f481c000000-7f481cfef000 rw-p 00000000 00:00 0

7f481cfef000-7f4820000000 ---p 00000000 00:00 0

7f4823c8d000-7f4823c8e000 ---p 00000000 00:00 0

7f4823c8e000-7f482448e000 rw-p 00000000 00:00 0 [stack:12610]

7f482448e000-7f482448f000 ---p 00000000 00:00 0

7f482448f000-7f4824c8f000 rw-p 00000000 00:00 0 [stack:12609]

7f4824c8f000-7f4824c90000 ---p 00000000 00:00 0

7f4824c90000-7f4825490000 rw-p 00000000 00:00 0 [stack:12608]

7f4825490000-7f4825491000 ---p 00000000 00:00 0

7f4825491000-7f4825c91000 rw-p 00000000 00:00 0 [stack:12606]

7f4825c91000-7f4825c92000 ---p 00000000 00:00 0

7f4825c92000-7f487770a000 rw-p 00000000 00:00 0 [stack:12607]

7f4e9e5da000-7f4e9e5db000 rw-s 00000000 00:05 360448 /SYSV17292eab (deleted)

7f4e9e5dc000-7f4e9e5de000 rw-p 00000000 00:00 0

7ffcd7aa4000-7ffcd7ad6000 rw-p 00000000 00:00 0 [stack]

7ffcd7baa000-7ffcd7bac000 r--p 00000000 00:00 0 [vvar]

7ffcd7bac000-7ffcd7bae000 r-xp 00000000 00:00 0 [vdso]

ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

Thank you,

Roberto

rspreafico

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Feb 23, 2016, 1:24:15 PM2/23/16

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I just tried the dynamic version, and that doesn't give this issue.

luca a

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Apr 28, 2017, 5:23:51 AM4/28/17

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Hi Alex,

I've just got the same: "Error in `STAR': double free or corruption (fasttop): 0x0000000001e46b30".

Could you confirm that if the "ALL DONE!" message is present in the Log.out the analysis has not been affected by this?
Is there any update on the correlation between static/dynamic/compiled version and the occurrence of this issue?
Log files attached for your convenience

Thanks,

Cheers

Luca

SRX1721419.Log.final.out

SRX1721419.Log.out

SRX1721419.Log.progress.out

Alexander Dobin

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Apr 28, 2017, 12:20:27 PM4/28/17

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Hi Luca,

the "ALL DONE" message indeed means that the run has been completed successfully, all files written and closed.

The error itself occurs when STAR exits and the system tries to free the allocated memory.

This is supposed to be fixed in 2.5.3a - please try it out.

Cheers

Alex

daniella apelblat

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Mar 9, 2020, 4:46:25 PM3/9/20

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Hi Alex,

I'm currently using version 2.5.3a and got this message as well.

The command I ran was:

STAR --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.05 --genomeDir STAR_index --readFilesIn sample.fastq --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic --runThreadN 20 --sjdbGTFfile genes.gtf --outFileNamePrefix sample --genomeLoad NoSharedMemory --sjdbGTFtagExonParentGene gene_name --outSAMattributes NH HI AS nM MD > sample.star.mapping.txt 2>&1

got the following result, do you have any idea what the issue is?

Mar 09 20:34:35 ..... started STAR run

Mar 09 20:34:35 ..... loading genome

Mar 09 20:35:26 ..... processing annotations GTF

Mar 09 20:35:28 ..... inserting junctions into the genome indices

Mar 09 20:37:04 ..... started 1st pass mapping

Mar 09 20:37:19 ..... finished 1st pass mapping

Mar 09 20:37:20 ..... inserting junctions into the genome indices

Mar 09 20:38:20 ..... started mapping

Mar 09 20:38:39 ..... started sorting BAM

EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree with the actual size on disk: 138746424 30748958 12