Entering edit mode
6.8 years ago
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..
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:
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.
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..
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.