Question: Cuffdiff fatal error exit code- 134 ()
0
gravatar for ananthikrish.rasi
10 weeks ago by
ananthikrish.rasi0 wrote:

Hi am getting the following error when I run galaxy cuff diff error..

Fatal error: Exit code 134 ()
[03:55:34] Loading reference annotation and sequence.
Warning: No conditions are replicated, switching to 'blind' dispersion method
[03:55:59] Inspecting maps and determining fragment length distributions.
[04:07:02] Modeling fragment count overdispersion.
 Map Properties:
    Normalized Map Mass: 13890865.58
    Raw Map Mass: 13882012.62
    Fragment Length Distribution: Empirical (learned)
                  Estimated Mean: 152.58
               Estimated Std Dev: 50.67
 Map Properties:
    Normalized Map Mass: 13890865.58
    Raw Map Mass: 12452642.58
    Fragment Length Distribution: Empirical (learned)
                  Estimated Mean: 47.00
               Estimated Std Dev: 0.09
 Map Properties:
    Normalized Map Mass: 13890865.58
    Raw Map Mass: 14694011.86
    Fragment Length Distribution: Empirical (learned)
                  Estimated Mean: 159.67
               Estimated Std Dev: 53.44
 Map Properties:
    Normalized Map Mass: 13890865.58
    Raw Map Mass: 14142158.79
    Fragment Length Distribution: Empirical (learned)
                  Estimated Mean: 168.93
               Estimated Std Dev: 56.92
 Map Properties:
    Normalized Map Mass: 13890865.58
    Raw Map Mass: 10357409.55
    Fragment Length Distribution: Empirical (learned)
                  Estimated Mean: 171.09
               Estimated Std Dev: 59.46
 Map Properties:
    Normalized Map Mass: 13890865.58
    Raw Map Mass: 18337742.53
    Fragment Length Distribution: Empirical (learned)
                  Estimated Mean: 166.71
               Estimated Std Dev: 53.72
 Map Properties:
    Normalized Map Mass: 13890865.58
    Raw Map Mass: 14697491.81
    Fragment Length Distribution: Empirical (learned)
                  Estimated Mean: 166.05
               Estimated Std Dev: 51.27
 Map Properties:
    Normalized Map Mass: 13890865.58
    Raw Map Mass: 14103028.69
    Fragment Length Distribution: Empirical (learned)
                  Estimated Mean: 163.38
               Estimated Std Dev: 53.52
[04:11:55] Calculating preliminary abundance estimates
Processed 18698 loci.                       
[05:22:24] Learning bias parameters.
[05:37:04] Testing for differential expression and regulation in locus.
*** glibc detected *** cuffdiff: double free or corruption (fasttop): 0x00007f63bd5d4c00 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3732075dee]
/lib64/libc.so.6[0x3732078c3d]
cuffdiff[0x41da11]
cuffdiff[0x42ab8a]
cuffdiff[0x4320a5]
cuffdiff[0x43501b]
cuffdiff[0x435b2a]
cuffdiff[0x41915a]
cuffdiff[0x54c3d9]
/lib64/libpthread.so.0[0x3732407aa1]
/lib64/libc.so.6(clone+0x6d)[0x37320e8bbd]
======= Memory map: ========
00400000-00653000 r-xp 00000000 00:18 112191                             /cvmfs/main.galaxyproject.org/deps/cufflinks/2.2.1/devteam/package_cufflinks_2_2_1/899067a260d1/bin/cuffdiff
00853000-00857000 rw-p 00253000 00:18 112191                             /cvmfs/main.galaxyproject.org/deps/cufflinks/2.2.1/devteam/package_cufflinks_2_2_1/899067a260d1/bin/cuffdiff
00857000-00878000 rw-p 00000000 00:00 0 
02490000-4c8cf000 rw-p 00000000 00:00 0                                  [heap]
3731c00000-3731c20000 r-xp 00000000 fd:00 46530567                       /lib64/ld-2.12.so
3731e1f000-3731e21000 r--p 0001f000 fd:00 46530567                       /lib64/ld-2.12.so
3731e21000-3731e22000 rw-p 00021000 fd:00 46530567                       /lib64/ld-2.12.so
3731e22000-3731e23000 rw-p 00000000 00:00 0 
3732000000-373218a000 r-xp 00000000 fd:00 46530593                       /lib64/libc-2.12.so
373218a000-373238a000 ---p 0018a000 fd:00 46530593                       /lib64/libc-2.12.so
373238a000-373238e000 r--p 0018a000 fd:00 46530593                       /lib64/libc-2.12.so
373238e000-3732390000 rw-p 0018e000 fd:00 46530593                       /lib64/libc-2.12.so
3732390000-3732394000 rw-p 00000000 00:00 0 
3732400000-3732417000 r-xp 00000000 fd:00 46530657                       /lib64/libpthread-2.12.so
3732417000-3732617000 ---p 00017000 fd:00 46530657                       /lib64/libpthread-2.12.so
3732617000-3732618000 r--p 00017000 fd:00 46530657                       /lib64/libpthread-2.12.so
3732618000-3732619000 rw-p 00018000 fd:00 46530657                       /lib64/libpthread-2.12.so
3732619000-373261d000 rw-p 00000000 00:00 0 
3733000000-3733015000 r-xp 00000000 fd:00 46530724                       /lib64/libz.so.1.2.3
3733015000-3733214000 ---p 00015000 fd:00 46530724                       /lib64/libz.so.1.2.3
3733214000-3733215000 r--p 00014000 fd:00 46530724                       /lib64/libz.so.1.2.3
3733215000-3733216000 rw-p 00015000 fd:00 46530724                       /lib64/libz.so.1.2.3
3733400000-3733483000 r-xp 00000000 fd:00 46530669                       /lib64/libm-2.12.so
3733483000-3733682000 ---p 00083000 fd:00 46530669                       /lib64/libm-2.12.so
3733682000-3733683000 r--p 00082000 fd:00 46530669                       /lib64/libm-2.12.so
3733683000-3733684000 rw-p 00083000 fd:00 46530669                       /lib64/libm-2.12.so
3736000000-3736016000 r-xp 00000000 fd:00 46530672                       /lib64/libgcc_s-4.4.7-20120601.so.1
3736016000-3736215000 ---p 00016000 fd:00 46530672                       /lib64/libgcc_s-4.4.7-20120601.so.1
3736215000-3736216000 rw-p 00015000 fd:00 46530672                       /lib64/libgcc_s-4.4.7-20120601.so.1
7f6370000000-7f6376cd4000 rw-p 00000000 00:00 0 
7f6376cd4000-7f6378000000 ---p 00000000 00:00 0 
7f6378000000-7f637a304000 rw-p 00000000 00:00 0 
7f637a304000-7f637c000000 ---p 00000000 00:00 0 
7f6380000000-7f6383fd7000 rw-p 00000000 00:00 0 
7f6383fd7000-7f6384000000 ---p 00000000 00:00 0 
7f6388000000-7f638bffb000 rw-p 00000000 00:00 0 
7f638bffb000-7f638c000000 ---p 00000000 00:00 0 
7f638c000000-7f6390000000 rw-p 00000000 00:00 0 
7f6390000000-7f6393d39000 rw-p 00000000 00:00 0 
7f6393d39000-7f6394000000 ---p 00000000 00:00 0 
7f6398000000-7f639c000000 rw-p 00000000 00:00 0 
7f63a0000000-7f63a4000000 rw-p 00000000 00:00 0 
7f63a8000000-7f63ac000000 rw-p 00000000 00:00 0 
7f63b0000000-7f63b8000000 rw-p 00000000 00:00 0 
7f63b8000000-7f63bbfff000 rw-p 00000000 00:00 0 
7f63bbfff000-7f63bc000000 ---p 00000000 00:00 0 
7f63bc000000-7f63bfe7f000 rw-p 00000000 00:00 0 
7f63bfe7f000-7f63c0000000 ---p 00000000 00:00 0 
7f63c0000000-7f63c296e000 rw-p 00000000 00:00 0 
7f63c296e000-7f63c4000000 ---p 00000000 00:00 0 
7f63c4000000-7f63c7fff000 rw-p 00000000 00:00 0 
7f63c7fff000-7f63c8000000 ---p 00000000 00:00 0 
7f63c8000000-7f63cffff000 rw-p 00000000 00:00 0 
7f63cffff000-7f63d0000000 ---p 00000000 00:00 0 
7f63d0000000-7f63d8000000 rw-p 00000000 00:00 0 
7f63d8000000-7f63db8d1000 rw-p 00000000 00:00 0 
7f63db8d1000-7f63dc000000 ---p 00000000 00:00 0 
7f63e0000000-7f63e3fef000 rw-p 00000000 00:00 0 
7f63e3fef000-7f63e4000000 ---p 00000000 00:00 0 
7f63e8000000-7f63ebce3000 rw-p 00000000 00:00 0 
7f63ebce3000-7f63ec000000 ---p 00000000 00:00 0 
7f63ec000000-7f63f0000000 rw-p 00000000 00:00 0 
7f63f0000000-7f63f4000000 rw-p 00000000 00:00 0 
7f63f8000000-7f63fc000000 rw-p 00000000 00:00 0 
7f63fc000000-7f63ff93a000 rw-p 00000000 00:00 0 
7f63ff93a000-7f6400000000 ---p 00000000 00:00 0 
7f6400000000-7f6403fff000 rw-p 00000000 00:00 0 
7f6403fff000-7f6404000000 ---p 00000000 00:00 0 
7f6408000000-7f640c000000 rw-p 00000000 00:00 0 
7f640c000000-7f6410000000 rw-p 00000000 00:00 0 
7f6410000000-7f6414000000 rw-p 00000000 00:00 0 
7f6414000000-7f6416962000 rw-p 00000000 00:00 0 
7f6416962000-7f6418000000 ---p 00000000 00:00 0 
7f6418000000-7f641bfff000 rw-p 00000000 00:00 0 
7f641bfff000-7f641c000000 ---p 00000000 00:00 0 
7f6420000000-7f6424000000 rw-p 00000000 00:00 0 
7f6424000000-7f6428000000 rw-p 00000000 00:00 0 
7f642c000000-7f642fe68000 rw-p 00000000 00:00 0 
7f642fe68000-7f6430000000 ---p 00000000 00:00 0 
7f6430000000-7f64336e3000 rw-p 00000000 00:00 0 
7f64336e3000-7f6434000000 ---p 00000000 00:00 0 
7f6434000000-7f6438000000 rw-p 00000000 00:00 0 
7f643c000000-7f6440000000 rw-p 00000000 00:00 0 
7f6440000000-7f6443f45000 rw-p 00000000 00:00 0 
7f6443f45000-7f6444000000 ---p 00000000 00:00 0 
7f6448000000-7f644c000000 rw-p 00000000 00:00 0 
7f644c000000-7f644ffff000 rw-p 00000000 00:00 0 
7f644ffff000-7f6450000000 ---p 00000000 00:00 0 
7f6454000000-7f6458000000 rw-p 00000000 00:00 0 
7f645c000000-7f645ff2c000 rw-p 00000000 00:00 0 
7f645ff2c000-7f6460000000 ---p 00000000 00:00 0 
7f6460000000-7f6463664000 rw-p 00000000 00:00 0 
7f6463664000-7f6464000000 ---p 00000000 00:00 0 
7f6464000000-7f6467ff9000 rw-p 00000000 00:00 0 
7f6467ff9000-7f6468000000 ---p 00000000 00:00 0 
7f646c000000-7f6470000000 rw-p 00000000 00:00 0 
7f6470000000-7f6474000000 rw-p 00000000 00:00 0 
7f6474000000-7f6477fd4000 rw-p 00000000 00:00 0 
7f6477fd4000-7f6478000000 ---p 00000000 00:00 0 
7f6478000000-7f647c000000 rw-p 00000000 00:00 0 
7f6480000000-7f6484000000 rw-p 00000000 00:00 0 
7f6484000000-7f6488000000 rw-p 00000000 00:00 0 
7f6488000000-7f648bcb7000 rw-p 00000000 00:00 0 
7f648bcb7000-7f648c000000 ---p 00000000 00:00 0 
7f648c000000-7f6490000000 rw-p 00000000 00:00 0 
7f6490000000-7f6493e40000 rw-p 00000000 00:00 0 
7f6493e40000-7f6494000000 ---p 00000000 00:00 0 
7f6498000000-7f649c000000 rw-p 00000000 00:00 0 
7f64a0000000-7f64a3e04000 rw-p 00000000 00:00 0 
7f64a3e04000-7f64a4000000 ---p 00000000 00:00 0 
7f64a5542000-7f64a5543000 ---p 00000000 00:00 0 
7f64a5543000-7f64a5f43000 rw-p 00000000 00:00 0 
7f64a5f43000-7f64a5f44000 ---p 00000000 00:00 0 
7f64a5f44000-7f64a6944000 rw-p 00000000 00:00 0 
7f64a6944000-7f64a6945000 ---p 00000000 00:00 0 
7f64a6945000-7f64a7345000 rw-p 00000000 00:00 0 
7f64a7345000-7f64a7346000 ---p 00000000 00:00 0 
7f64a7346000-7f64a7d46000 rw-p 00000000 00:00 0 
7f64a8747000-7f64a8748000 ---p 00000000 00:00 0 
7f64a8748000-7f64a9148000 rw-p 00000000 00:00 0 
7f64a9148000-7f64a9149000 ---p 00000000 00:00 0 
7f64a9149000-7f64a9d4d000 rw-p 00000000 00:00 0 
7f64a9d56000-7f64a9d58000 rw-p 00000000 00:00 0 
7fff10ac6000-7fff10ae1000 rw-p 00000000 00:00 0                          [stack]
7fff10b7b000-7fff10b7c000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
/galaxy-repl/main/jobdir/016/307/16307505/tool_script.sh: line 9:  9570 Aborted                 (core dumped) cuffdiff --no-update-check --quiet --FDR=0.05 --num-threads="${GALAXY_SLOTS:-4}" --min-alignment-count=10 --library-norm-method=geometric --dispersion-method=blind -b "/galaxy/data/hg19/sam_index/hg19.fa" --labels 'Control_1','Control_2','Control_3','Control_4','Test_1','Test_2','Test_3','Test_4' /galaxy-repl/main/files/020/573/dataset_20573651.dat /galaxy-repl/main/files/020/499/dataset_20499563.dat /galaxy-repl/main/files/020/510/dataset_20510007.dat /galaxy-repl/main/files/020/541/dataset_20541040.dat /galaxy-repl/main/files/020/550/dataset_20550346.dat /galaxy-repl/main/files/020/499/dataset_20499605.dat /galaxy-repl/main/files/020/510/dataset_20510772.dat /galaxy-repl/main/files/020/542/dataset_20542627.dat /galaxy-repl/main/files/020/571/dataset_20571230.dat

Kindly clarify this. Thank you..

rna-seq • 166 views
ADD COMMENTlink modified 10 weeks ago by Istvan Albert ♦♦ 73k • written 10 weeks ago by ananthikrish.rasi0

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

You should also know that the old 'Tuxedo' pipeline of Tophat and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.) There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using kallisto or salmon.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by WouterDeCoster21k

Can you please give me the full version of this paper? I cant access my email id: ananthikrish.rasi@gmail.com Thank you so much..

ADD REPLYlink written 10 weeks ago by ananthikrish.rasi0

Google for double free or corruption (fasttop), you will find plenty of answers. Long story short, it seems like a bug. The Tuxedo suite has been retired (I am too lazy to search for the original announcement, but see C: number of threads for cufflinks transcript assembly ), even so you may try to open a ticket at Cufflinks GitHub page.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by h.mon8.7k
0
gravatar for Istvan Albert
10 weeks ago by
Istvan Albert ♦♦ 73k
University Park, USA
Istvan Albert ♦♦ 73k wrote:

As h.mon mentions the Tuxedo suite has been retired. See C: number of threads for cufflinks transcript assembly by WouterDeCoster for alternatives.

As for your specific problem, if you must keep using the Tuxedo suite then using an older version of the tool (hence even more obsolete) or a different operating system might avoid triggering the bug. Though clearly, the program is not performing correctly and all results produced by it may be unreliable.

ADD COMMENTlink written 10 weeks ago by Istvan Albert ♦♦ 73k
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