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STAR: free(): invalid next size (normal) error in STAR v2.7.5a #955

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Kailewang opened this issue Jun 25, 2020 · 8 comments
Closed

STAR: free(): invalid next size (normal) error in STAR v2.7.5a #955

Kailewang opened this issue Jun 25, 2020 · 8 comments
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issue: usage

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@Kailewang
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Hi,

I meet this problem when I run STAR v2.7.3a, and I also tried STAR v2.7.5a, also got same error (see below output files).

Jun 24 23:27:19 ..... started STAR run
Jun 24 23:27:19 ..... loading genome
Jun 24 23:27:37 ..... started mapping
Jun 24 23:31:04 ..... finished mapping
Jun 24 23:31:06 ..... started Solo counting
*** Error in `/volumes/seq/code/3rd_party/STAR/STAR-2.7.5a/bin/Linux_x86_64/STAR': free(): invalid next size (normal): 0x0000000068a7d0b0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x7fa96343e489]
/lib64/libc.so.6(qsort_r+0x2d8)[0x7fa9633f5fe8]
/volumes/seq/code/3rd_party/STAR/STAR-2.7.5a/bin/Linux_x86_64/STAR[0x43ea40]
/volumes/seq/code/3rd_party/STAR/STAR-2.7.5a/bin/Linux_x86_64/STAR[0x426cdd]
/volumes/seq/code/3rd_party/STAR/STAR-2.7.5a/bin/Linux_x86_64/STAR[0x4423e0]
/volumes/seq/code/3rd_party/STAR/STAR-2.7.5a/bin/Linux_x86_64/STAR[0x43c605]
/volumes/seq/code/3rd_party/STAR/STAR-2.7.5a/bin/Linux_x86_64/STAR[0x40cf4f]
/lib64/libc.so.6(libc_start_main+0xf5)[0x7fa9633df3d5]
/volumes/seq/code/3rd_party/STAR/STAR-2.7.5a/bin/Linux_x86_64/STAR[0x417d45]
======= Memory map: ========
00400000-00588000 r-xp 00000000 08:21 2599815550 /volumes/seq/code/3rd_party/STAR/STAR-2.7.5a/bin/Linux_x86_64/STAR
00787000-00788000 r--p 00187000 08:21 2599815550 /volumes/seq/code/3rd_party/STAR/STAR-2.7.5a/bin/Linux_x86_64/STAR
00788000-00794000 rw-p 00188000 08:21 2599815550 /volumes/seq/code/3rd_party/STAR/STAR-2.7.5a/bin/Linux_x86_64/STAR
00794000-00797000 rw-p 00000000 00:00 0
024f1000-699e2000 rw-p 00000000 00:00 0 [heap]
7fa404000000-7fa404021000 rw-p 00000000 00:00 0
7fa404021000-7fa408000000 ---p 00000000 00:00 0
7fa40c000000-7fa40c4bf000 rw-p 00000000 00:00 0
7fa40c4bf000-7fa410000000 ---p 00000000 00:00 0
7fa410000000-7fa4104bf000 rw-p 00000000 00:00 0
7fa4104bf000-7fa414000000 ---p 00000000 00:00 0
7fa414000000-7fa4144c2000 rw-p 00000000 00:00 0
7fa4144c2000-7fa418000000 ---p 00000000 00:00 0
7fa418000000-7fa418021000 rw-p 00000000 00:00 0
7fa418021000-7fa41c000000 ---p 00000000 00:00 0
7fa41c000000-7fa41c4c2000 rw-p 00000000 00:00 0
7fa41c4c2000-7fa420000000 ---p 00000000 00:00 0
7fa420000000-7fa4204c1000 rw-p 00000000 00:00 0
7fa4204c1000-7fa424000000 ---p 00000000 00:00 0
7fa424000000-7fa4244be000 rw-p 00000000 00:00 0
7fa4244be000-7fa428000000 ---p 00000000 00:00 0
7fa428000000-7fa4284c5000 rw-p 00000000 00:00 0
7fa4284c5000-7fa42c000000 ---p 00000000 00:00 0
7fa42c000000-7fa42c4c1000 rw-p 00000000 00:00 0
7fa42c4c1000-7fa430000000 ---p 00000000 00:00 0
7fa430000000-7fa4304c6000 rw-p 00000000 00:00 0
7fa4304c6000-7fa434000000 ---p 00000000 00:00 0
7fa434000000-7fa4344c1000 rw-p 00000000 00:00 0
7fa4344c1000-7fa438000000 ---p 00000000 00:00 0
7fa438000000-7fa4384c2000 rw-p 00000000 00:00 0
7fa4384c2000-7fa43c000000 ---p 00000000 00:00 0
7fa43c000000-7fa43c4ca000 rw-p 00000000 00:00 0
7fa43c4ca000-7fa440000000 ---p 00000000 00:00 0
7fa440000000-7fa4404c2000 rw-p 00000000 00:00 0
7fa4404c2000-7fa444000000 ---p 00000000 00:00 0
7fa444000000-7fa4444cd000 rw-p 00000000 00:00 0
7fa4444cd000-7fa448000000 ---p 00000000 00:00 0
7fa448000000-7fa4484ce000 rw-p 00000000 00:00 0
7fa4484ce000-7fa44c000000 ---p 00000000 00:00 0
7fa44c000000-7fa44c4c2000 rw-p 00000000 00:00 0
7fa44c4c2000-7fa450000000 ---p 00000000 00:00 0
7fa450000000-7fa4504c0000 rw-p 00000000 00:00 0
7fa4504c0000-7fa454000000 ---p 00000000 00:00 0
7fa454000000-7fa4544b1000 rw-p 00000000 00:00 0
7fa4544b1000-7fa458000000 ---p 00000000 00:00 0
7fa458000000-7fa458021000 rw-p 00000000 00:00 0
7fa458021000-7fa45c000000 ---p 00000000 00:00 0
7fa45c000000-7fa45c4c3000 rw-p 00000000 00:00 0
7fa45c4c3000-7fa460000000 ---p 00000000 00:00 0
7fa460000000-7fa4604c3000 rw-p 00000000 00:00 0
7fa4604c3000-7fa464000000 ---p 00000000 00:00 0
7fa464000000-7fa4644c0000 rw-p 00000000 00:00 0
7fa4644c0000-7fa468000000 ---p 00000000 00:00 0
7fa468000000-7fa4684c3000 rw-p 00000000 00:00 0
7fa4684c3000-7fa46c000000 ---p 00000000 00:00 0
7fa46c000000-7fa46c4c4000 rw-p 00000000 00:00 0
7fa46c4c4000-7fa470000000 ---p 00000000 00:00 0
7fa470000000-7fa4704be000 rw-p 00000000 00:00 0
7fa4704be000-7fa474000000 ---p 00000000 00:00 0
7fa474000000-7fa474021000 rw-p 00000000 00:00 0
7fa474021000-7fa478000000 ---p 00000000 00:00 0
7fa478000000-7fa4784c5000 rw-p 00000000 00:00 0
7fa4784c5000-7fa47c000000 ---p 00000000 00:00 0
7fa47c000000-7fa47c021000 rw-p 00000000 00:00 0
7fa47c021000-7fa480000000 ---p 00000000 00:00 0
7fa480000000-7fa4804c4000 rw-p 00000000 00:00 0
7fa4804c4000-7fa484000000 ---p 00000000 00:00 0
7fa484000000-7fa484021000 rw-p 00000000 00:00 0
7fa484021000-7fa488000000 ---p 00000000 00:00 0
7fa488000000-7fa488021000 rw-p 00000000 00:00 0
7fa488021000-7fa48c000000 ---p 00000000 00:00 0
7fa48c000000-7fa48c021000 rw-p 00000000 00:00 0
7fa48c021000-7fa490000000 ---p 00000000 00:00 0
7fa490000000-7fa490021000 rw-p 00000000 00:00 0
7fa490021000-7fa494000000 ---p 00000000 00:00 0
7fa494000000-7fa494021000 rw-p 00000000 00:00 0
7fa494021000-7fa498000000 ---p 00000000 00:00 0
7fa498000000-7fa498021000 rw-p 00000000 00:00 0
7fa498021000-7fa49c000000 ---p 00000000 00:00 0
7fa49c000000-7fa49c021000 rw-p 00000000 00:00 0
7fa49c021000-7fa4a0000000 ---p 00000000 00:00 0
7fa4a0fe2000-7fa4a0fe3000 ---p 00000000 00:00 0
7fa4a0fe3000-7fa4a17e3000 rw-p 00000000 00:00 0
7fa4a17e3000-7fa4a17e4000 ---p 00000000 00:00 0
7fa4a17e4000-7fa4a1fe4000 rw-p 00000000 00:00 0
7fa4a1fe4000-7fa4a1fe5000 ---p 00000000 00:00 0
7fa4a1fe5000-7fa4a27e5000 rw-p 00000000 00:00 0
7fa4a27e5000-7fa4a27e6000 ---p 00000000 00:00 0
7fa4a27e6000-7fa4a2fe6000 rw-p 00000000 00:00 0
7fa4b0000000-7fa4b0021000 rw-p 00000000 00:00 0
7fa4b0021000-7fa4b4000000 ---p 00000000 00:00 0
7fa4b8972000-7fa643335000 rw-p 00000000 00:00 0
7fa8f7d0c000-7fa90d9a0000 rw-p 00000000 00:00 0
7fa925ef9000-7fa9633bd000 rw-p 00000000 00:00 0
7fa9633bd000-7fa96357f000 r-xp 00000000 fd:00 4295359169 /usr/lib64/libc-2.17.so
7fa96357f000-7fa96377f000 ---p 001c2000 fd:00 4295359169 /usr/lib64/libc-2.17.so
7fa96377f000-7fa963783000 r--p 001c2000 fd:00 4295359169 /usr/lib64/libc-2.17.so
7fa963783000-7fa963785000 rw-p 001c6000 fd:00 4295359169 /usr/lib64/libc-2.17.so
7fa963785000-7fa96378a000 rw-p 00000000 00:00 0
7fa96378a000-7fa9637a1000 r-xp 00000000 fd:00 4295359195 /usr/lib64/libpthread-2.17.so
7fa9637a1000-7fa9639a0000 ---p 00017000 fd:00 4295359195 /usr/lib64/libpthread-2.17.so
7fa9639a0000-7fa9639a1000 r--p 00016000 fd:00 4295359195 /usr/lib64/libpthread-2.17.so
7fa9639a1000-7fa9639a2000 rw-p 00017000 fd:00 4295359195 /usr/lib64/libpthread-2.17.so
7fa9639a2000-7fa9639a6000 rw-p 00000000 00:00 0
7fa9639a6000-7fa9639bb000 r-xp 00000000 fd:00 4302262397 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fa9639bb000-7fa963bba000 ---p 00015000 fd:00 4302262397 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fa963bba000-7fa963bbb000 r--p 00014000 fd:00 4302262397 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fa963bbb000-7fa963bbc000 rw-p 00015000 fd:00 4302262397 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fa963bbc000-7fa963be1000 r-xp 00000000 fd:00 4296036295 /usr/lib64/libgomp.so.1.0.0process-star.sh: line 38: 138925 Aborted (core dumped) /volumes/seq/code/3rd_party/STAR/STAR-2.7.5a/bin/Linux_x86_64/STAR --runThreadN 40 --genomeDir $REF_Genome --readFilesIn $RNAPATH/trimmed_paired$NAME_S1_L001_R2_001.fastq.gz $RNAPATH/trimmed_paired$NAME_S1_L001_R1_001.fastq.gz --readFilesCommand zcat --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix $NAME_ --soloType CB_UMI_Simple --soloCBwhitelist /volumes/lab/users/wangkl/wsc/barcode/com_index_bc.txt --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 10 --soloUMIfiltering MultiGeneUMI --soloCBmatchWLtype 1MM_multi_pseudocounts --soloFeatures Gene GeneFull SJ Velocyto

Logs.zip
@alexdobin
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Hi Kaile,

a few things to try first:

  1. Please try to run static executable from Linux_x86_64_static/STAR
  2. The problem is happening at the SJ counting stage - please try to remove SJ from --soloFeatures

Cheers
Alex

@Kailewang
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Thanks! It works after I remove SJ.

@alexdobin
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Hi Kaile,

a couple of more things that will help me debug this problem - does it break if

  1. You use just SJ, i.e. --soloFeatures SJ, does it still happen.
  2. You use a small subset of reads with --readMapNumber 100000

Cheers
Alex

@Kailewang
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Thanks! I tried only use SJ, it gave me Segmentation fault error, see below. I also tried only use 100000 reads with only SJ, still get the same errors.

Jun 25 12:23:26 ..... started STAR run
Jun 25 12:23:26 ..... loading genome
Jun 25 12:23:42 ..... started mapping
Jun 25 12:27:38 ..... finished mapping
Jun 25 12:27:41 ..... started Solo counting
process-star-bugtest.sh: line 38: 151037 Segmentation fault      (core dumped) /volumes/seq/code/3rd_party/STAR/STAR-2.7.3a/bin/Linux_x86_64/STAR --runThreadN 40 --genomeDir $REF_Genome --readFilesIn $RNAPATH/trimmed_paired_$NAME\_S1_L001_R2_001.fastq.gz $RNAPATH/trimmed_paired_$NAME\_S1_L001_R1_001.fastq.gz --readFilesCommand zcat --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix $NAME\_ --soloType CB_UMI_Simple --soloCBwhitelist /volumes/lab/users/wangkl/wsc/barcode/com_index_bc.txt --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 10 --soloUMIfiltering MultiGeneUMI --soloCBmatchWLtype 1MM_multi_pseudocounts --soloFeatures SJ

OnlySJ_Log.zip

@alexdobin
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Hi Kaile,

thanks a lot for the tests! Would you be able to share the 100k reads that caused the seg-fault, so that I can reproduce the problem and fix it?

Cheers
Alex

@Kailewang
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That would be great! Could you share me your email address? you can connect me by llee90504452@gmail.com

@alexdobin
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Hi Kaile,

thanks for the test files. I think I fixed the bug, please try the latest patch from Github master on the full dataset.

Cheers
Alex

@alexdobin
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Hi Kalie,

thanks a lot for the bug report!
The patch is released in 2.7.5b .

Cheers
Alex

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@alexdobin @Kailewang