[BioC] Rsubread segfault
James W. MacDonald
jmacdon at uw.edu
Tue Oct 22 22:51:07 CEST 2013
I am getting a segfault with Rsubread. It appears to finish, but then
segfaults and kills R.
> library(Rsubread)
> fls <- paste0("../data/", dir("../data/", "sam$"))
> dat <- featureCounts(fls, annot.inbuilt = "mm10")
Mouse annotation NCBI Build 38.1 is used.
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 1.12.0
//========================== featureCounts setting
===========================\\
|| ||
|| Input files : 24 SAM
files ||
|| o
../data/RCP12.sam ||
|| o
../data/RCP14.sam ||
|| o
../data/RCP16.sam ||
|| o
../data/RCP1_REPEAT.sam ||
|| o
../data/RCP20_REPEAT.sam ||
|| o
../data/RCP21.sam ||
|| o
../data/RCP22.sam ||
|| o
../data/RCP2.sam ||
|| o
../data/RCP3.sam ||
|| o
../data/RCP6.sam ||
|| o
../data/RCP7.sam ||
|| o
../data/RCP9.sam ||
|| o
../data/RUP13.sam ||
|| o
../data/RUP15_REPEAT.sam ||
|| o
../data/RUP17.sam ||
|| o
../data/RUP19.sam ||
|| o
../data/RUP1.sam ||
|| o
../data/RUP20.sam ||
|| o
../data/RUP22_REPEAT.sam ||
|| o
../data/RUP23.sam ||
|| o
../data/RUP24.sam ||
|| o
../data/RUP25.sam ||
|| o
../data/RUP26.sam ||
|| o
../data/RUP27.sam ||
|| ||
|| Output file :
./.Rsubread_featureCounts_pid30445 ||
|| Annotations :
/data/programs/lib64/R/library/Rsubread/anno ... ||
|| ||
|| Threads :
1 ||
|| Level : meta-feature
level ||
|| Paired-end :
no ||
|| Strand specific :
no ||
|| Multimapping reads : not
counted ||
|| Multi-overlapping reads : not
counted ||
|| ||
\\===================== http://subread.sourceforge.net/
======================//
//================================= Running
==================================\\
|| ||
|| Load annotation file
/data/programs/lib64/R/library/Rsubread/annot/mm1 ... ||
|| Number of features is
222996 ||
|| Number of meta-features is
27179 ||
|| Number of chromosomes is
43 ||
<snip>
|| Process ../data/RUP27.sam
... ||
|| Total number of reads is :
12363805 ||
|| Number of successfully assigned reads is : 6077652
(49.2%) ||
|| Running time : 0.12
minutes ||
|| ||
|| Read assignment
finished. ||
|| ||
\\===================== http://subread.sourceforge.net/
======================//
*** Error in `/data/programs/lib64/R/bin/exec/R': double free or
corruption (!prev): 0x0000000001e2f8f0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7aa26)[0x7f7ddc4e3a26]
/lib/x86_64-linux-gnu/libc.so.6(+0x7b7a3)[0x7f7ddc4e47a3]
/data/programs/lib64/R/library/Rsubread/libs/Rsubread.so(R_readSummary_wrapper+0x110)[0x7f7ddae9eac0]
/data/programs/lib64/R/bin/exec/R[0x475226]
/data/programs/lib64/R/bin/exec/R(Rf_eval+0x5db)[0x4aefcb]
/data/programs/lib64/R/bin/exec/R[0x4b1d90]
/data/programs/lib64/R/bin/exec/R(Rf_eval+0x441)[0x4aee31]
/data/programs/lib64/R/bin/exec/R[0x4b1f50]
/data/programs/lib64/R/bin/exec/R(Rf_eval+0x441)[0x4aee31]
/data/programs/lib64/R/bin/exec/R(Rf_applyClosure+0x34b)[0x4a16cb]
/data/programs/lib64/R/bin/exec/R(Rf_eval+0x1ee)[0x4aebde]
/data/programs/lib64/R/bin/exec/R[0x4b1d90]
/data/programs/lib64/R/bin/exec/R(Rf_eval+0x441)[0x4aee31]
/data/programs/lib64/R/bin/exec/R[0x4b1f50]
/data/programs/lib64/R/bin/exec/R(Rf_eval+0x441)[0x4aee31]
/data/programs/lib64/R/bin/exec/R(Rf_eval+0x441)[0x4aee31]
/data/programs/lib64/R/bin/exec/R(Rf_ReplIteration+0x229)[0x4d0d99]
/data/programs/lib64/R/bin/exec/R[0x4d0ff9]
/data/programs/lib64/R/bin/exec/R(run_Rmainloop+0x41)[0x4d14b1]
/data/programs/lib64/R/bin/exec/R(main+0x18)[0x415c38]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f7ddc48a995]
/data/programs/lib64/R/bin/exec/R[0x415b49]
======= Memory map: ========
00400000-00679000 r-xp 00000000 08:21 100622427
/data/programs/lib64/R/bin/exec/R
00878000-00883000 rw-p 00278000 08:21 100622427
/data/programs/lib64/R/bin/exec/R
00883000-0096e000 rw-p 00000000 00:00 0
01114000-02f0a000 rw-p 00000000 00:00 0
[heap]
7f7dda193000-7f7dda1aa000 r-xp 00000000 08:11 21415
/lib/x86_64-linux-gnu/libz.so.1.2.8
7f7dda1aa000-7f7dda3a9000 ---p 00017000 08:11 21415
/lib/x86_64-linux-gnu/libz.so.1.2.8
7f7dda3a9000-7f7dda3aa000 r--p 00016000 08:11 21415
/lib/x86_64-linux-gnu/libz.so.1.2.8
7f7dda3aa000-7f7dda3ab000 rw-p 00017000 08:11 21415
/lib/x86_64-linux-gnu/libz.so.1.2.8
7f7dda3ab000-7f7dda560000 r-xp 00000000 08:21 100515846
/data/programs/lib64/R/lib/libRlapack.so
7f7dda560000-7f7dda75f000 ---p 001b5000 08:21 100515846
/data/programs/lib64/R/lib/libRlapack.so
7f7dda75f000-7f7dda761000 rw-p 001b4000 08:21 100515846
/data/programs/lib64/R/lib/libRlapack.so
7f7dda761000-7f7dda7fa000 r-xp 00000000 08:21 100524323
/data/programs/lib64/R/library/stats/libs/stats.so
7f7dda7fa000-7f7dda9fa000 ---p 00099000 08:21 100524323
/data/programs/lib64/R/library/stats/libs/stats.so
7f7dda9fa000-7f7dda9fd000 rw-p 00099000 08:21 100524323
/data/programs/lib64/R/library/stats/libs/stats.so
7f7dda9fd000-7f7dda9fe000 rw-p 00000000 00:00 0
7f7dda9fe000-7f7ddaa3c000 r-xp 00000000 08:21 100573350
/data/programs/lib64/R/library/graphics/libs/graphics.so
7f7ddaa3c000-7f7ddac3b000 ---p 0003e000 08:21 100573350
/data/programs/lib64/R/library/graphics/libs/graphics.so
7f7ddac3b000-7f7ddac3d000 rw-p 0003d000 08:21 100573350
/data/programs/lib64/R/library/graphics/libs/graphics.so
7f7ddac3d000-7f7ddac79000 r-xp 00000000 08:21 100524653
/data/programs/lib64/R/library/grDevices/libs/grDevices.so
7f7ddac79000-7f7ddae79000 ---p 0003c000 08:21 100524653
/data/programs/lib64/R/library/grDevices/libs/grDevices.so
7f7ddae79000-7f7ddae7f000 rw-p 0003c000 08:21 100524653
/data/programs/lib64/R/library/grDevices/libs/grDevices.so
7f7ddae7f000-7f7ddae80000 rw-p 00000000 00:00 0
7f7ddae90000-7f7ddaeee000 r-xp 00000000 08:21 103170387
/data/programs/lib64/R/library/Rsubread/libs/Rsubread.so
7f7ddaeee000-7f7ddb0ed000 ---p 0005e000 08:21 103170387
/data/programs/lib64/R/library/Rsubread/libs/Rsubread.so
7f7ddb0ed000-7f7ddb0ef000 rw-p 0005d000 08:21 103170387
/data/programs/lib64/R/library/Rsubread/libs/Rsubread.so
7f7ddb0ef000-7f7ddb0fa000 rw-p 00000000 00:00 0
7f7ddb0fa000-7f7ddb0fc000 r-xp 00000000 08:15 124401
/usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f7ddb0fc000-7f7ddb2fb000 ---p 00002000 08:15 124401
/usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f7ddb2fb000-7f7ddb2fc000 r--p 00001000 08:15 124401
/usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f7ddb2fc000-7f7ddb2fd000 rw-p 00002000 08:15 124401
/usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f7ddb2fd000-7f7ddb406000 rw-p 00000000 00:00 0
7f7ddb406000-7f7ddb40d000 r-xp 00000000 08:21 100606286
/data/programs/lib64/R/library/methods/libs/methods.so
7f7ddb40d000-7f7ddb60d000 ---p 00007000 08:21 100606286
/data/programs/lib64/R/library/methods/libs/methods.so
7f7ddb60d000-7f7ddb60e000 rw-p 00007000 08:21 100606286
/data/programs/lib64/R/library/methods/libs/methods.so
7f7ddb60e000-7f7ddb618000 r-xp 00000000 08:21 100566155
/data/programs/lib64/R/library/utils/libs/utils.so
7f7ddb618000-7f7ddb818000 ---p 0000a000 08:21 100566155
/data/programs/lib64/R/library/utils/libs/utils.so
7f7ddb818000-7f7ddb819000 rw-p 0000a000 08:21 100566155
/data/programs/lib64/R/library/utils/libs/utils.so
7f7ddb819000-7f7ddb81a000 rw-p 00000000 00:00 0
7f7ddb81a000-7f7ddb821000 r-xp 00000000 08:11 21551
/lib/x86_64-linux-gnu/libnss_sss.so.2
7f7ddb821000-7f7ddba20000 ---p 00007000 08:11 21551
/lib/x86_64-linux-gnu/libnss_sss.so.2
7f7ddba20000-7f7ddba21000 r--p 00006000 08:11 21551
/lib/x86_64-linux-gnu/libnss_sss.so.2
7f7ddba21000-7f7ddba22000 rw-p 00007000 08:11 21551
/lib/x86_64-linux-gnu/libnss_sss.so.2
7f7ddba22000-7f7ddba2e000 r-xp 00000000 08:11 21617
/lib/x86_64-linux-gnu/libnss_files-2.17.so
7f7ddba2e000-7f7ddbc2d000 ---p 0000c000 08:11 21617
/lib/x86_64-linux-gnu/libnss_files-2.17.so
7f7ddbc2d000-7f7ddbc2e000 r--p 0000b000 08:11 21617
/lib/x86_64-linux-gnu/libnss_files-2.17.so
7f7ddbc2e000-7f7ddbc2f000 rw-p 0000c000 08:11 21617
/lib/x86_64-linux-gnu/libnss_files-2.17.so
7f7ddbc2f000-7f7ddbdd8000 rw-p 00000000 00:00 0
7f7ddbdd8000-7f7ddbe1a000 r-xp 00000000 08:11 23573
/lib/libncurses.so.5.7
7f7ddbe1a000-7f7ddc019000 ---p 00042000 08:11 23573
/lib/libncurses.so.5.7
7f7ddc019000-7f7ddc01e000 rw-p 00041000 08:11 23573
/lib/libncurses.so.5.7
7f7ddc01e000-7f7ddc033000 r-xp 00000000 08:11 21583
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f7ddc033000-7f7ddc233000 ---p 00015000 08:11 21583
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f7ddc233000-7f7ddc234000 rw-p 00015000 08:11 21583
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f7ddc234000-7f7ddc269000 r-xp 00000000 08:15 458903
/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f7ddc269000-7f7ddc468000 ---p 00035000 08:15 458903
/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f7ddc468000-7f7ddc469000 rw-p 00034000 08:15 458903
/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f7ddc469000-7f7ddc60b000 r-xp 00000000 08:11 21566
/lib/x86_64-linux-gnu/libc-2.17.so
7f7ddc60b000-7f7ddc80b000 ---p 001a2000 08:11 21566
/lib/x86_64-linux-gnu/libc-2.17.so
7f7ddc80b000-7f7ddc80f000 r--p 001a2000 08:11 21566
/lib/x86_64-linux-gnu/libc-2.17.so
7f7ddc80f0
Process /data/programs/bin/R aborted at Tue Oct 22 12:34:40 2013
And after restarting,
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rsubread_1.12.0
loaded via a namespace (and not attached):
[1] compiler_3.0.2 tools_3.0.2
If I split the files up into groups of eight, I could get featureCounts
to run. Also please note that I am using the current version of Subread:
jmacdon$ subread-align
Version 1.4.0
Best,
Jim
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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