the boost build system for 1.5.5 (the version we need to use currently) doesn't recognize address_mode=# as a valid input

it needs a dash instead of an underscore, that rectified it.

Hi Guys,
Following "Installing a pre-compiled binary release" (http://cole-trapnell-lab.github.io/cufflinks/getting_started/#installing-a-pre-compiled-binary-release), I downloaded the pre-compiled ZIP file cufflinks-master.zip and unzipped it, however I can not find the cufflinks,cuffdiff and cuffcompare binaries files in the folder.
What should I do?

Thanks in advance!

I encountered some problem when running cufflinks 2.2.1 on some sequencing data with very high coverage. When run with default setting --max-bundle-frags 1000000 , the locus with high abundance is not present in the transcripts.gtf and not in skipped.gtf either. When run with --max-bundle-frags 10000000 , the locus is reported in transcripts.gtf and the estimated absolute depth of read coverage across the whole transcript is ~55000 . The manual states that loci skipped due to --max-bundle-frags limit will be listed in skipped.gtf .

Has anyone experienced this issue? Hope it can be fixed soon if it's indeed an unexpected behavior of cufflinks.

I am on an up to date Arch Linux with boost 1.57.0. cufflinks compilation fails at target abundances.o with the following errors (this is the output of clang++ which I find nicer visually better than g++):

In file included from abundances.cpp:16:
In file included from ./abundances.h:17:
In file included from /usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/vector:60:
In file included from /usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/bits/stl_algobase.h:64:
/usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/bits/stl_pair.h:119:22: error: no matching constructor for initialization of 'boost::shared_ptr<void>'
        : first(__p.first), second(__p.second) { }
                            ^      ~~~~~~~~~~

In file included from abundances.cpp:16:
In file included from ./abundances.h:17:
In file included from /usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/vector:60:
In file included from /usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/bits/stl_algobase.h:64:
/usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/bits/stl_pair.h:119:22: error: no matching constructor for initialization of 'boost::shared_ptr<void>'
        : first(__p.first), second(__p.second) { }
                            ^      ~~~~~~~~~~

I presume errors like these may occur in other places as well.

It failed in stl_pair.h:119:39: error: no matching function for call to ‘boost::shared_ptr
see https://bugs.gentoo.org/show_bug.cgi?id=535716 for the full error msg.

Have the current version of cufflinks from git. No tags, so I'm using master (last commit 815e435 from Jan 10).

Attempting to build on Ubuntu 12.04.5 LTS, Boost v1.49.0. Eigen 5097c01bcdc4. gcc 4.6.3. Automake v1.11.3.

./configure --prefix=/usr/local --with-boost=~/src/boost --with-bam=~/src/samtool_libs --with-eigen=~/src/eigen/Eigen

 configure: error: cannot find sources (config.h.in) in . or ..

Any thoughts? Currently have cufflinks v2.1.1 installed, and it had no issues building that version on the same system.

From Bob Zimmerman:

"I’m running cufflinks on a scaffolded genome. Therefore some transcripts are actually split by the ends of scaffolds. Cufflinks reports a few transcripts as having ends greater than the lengths of the scaffolds, I imagine because the start plus the length of the aligned read goes off the end. This causes the PASA pipeline to crash, and can cause other such scripts to fail. As the BAM file contains the lengths of each scaffold, would it be possible to enforce that this doesn’t happen?"

is cufflinks going to break from external samtools like tophat did? samtools split into 3 projects now, though it still compiles much the same way (if you pull the repos and attempt to build samtools it seem to automatically try to depend on the other libraries and assumes they're in the same directory if you don't give it a path manually).

I don't mind if it does, but just try to be careful not to break the ability to do an out-of-source build like tophat did.

When I configure cufflinks on CentOS 7 with libbam installed in '/usr/local/' I get the following error:

checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in bam/version.hpp. See http://randspringer.de/bam for more documentation.

After tracking down the issue and making sure permissions where set correctly I realised that there is no "version.hpp". I downloaded Samtools 1.1 and it contains "version.h". Changing the configure file fixed the issue and cufflinks compiled correctly. Is this a bug or am I compiling Cufflinks incorrectly?

Thanks in advance,
Ken

Line 91 in : https://github.com/cole-trapnell-lab/cufflinks/blob/master/src/cuffquant.cpp

It gives the usage information for cuffDIFF, not cuffQUANT. In particular, it says that cuffquant supports multiple different BAM/SAM samples, comma-delimited which appears not to be the case according to the help on the web.

I detected a bug in gffread when converting gff3 to gtf using Cufflinks v.2.2.1 on Linux.

The gff3 file called all.gff3 can be downloaded from here:
ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/

This file was converted to gtf using gffread:

$ gffread all.gff3 -T -o all.gtf

Check the exon coordinates of transcript LOC_Os06g46770.3 in gff3 file:

$ grep LOC_Os06g46770.3 all.gff3 | grep exon

Chr6 MSU_osa1r7 exon 28401731 28401808 . + . ID=LOC_Os06g46770.3:exon_1;Parent=LOC_Os06g46770.3
Chr6 MSU_osa1r7 exon 28402585 28403489 . + . ID=LOC_Os06g46770.3:exon_2;Parent=LOC_Os06g46770.3
Chr6 MSU_osa1r7 exon 28403718 28404585 . + . ID=LOC_Os06g46770.3:exon_3;Parent=LOC_Os06g46770.3

Then check the same in a new gtf file:

$ grep LOC_Os06g46770.3 all.gtf | grep exon

Chr6 MSU_osa1r7 exon 28401731 28401808 . + . transcript_id "LOC_Os06g46770.3"; gene_id "LOC_Os06g46770"; gene_name "LOC_Os06g46770";
Chr6 MSU_osa1r7 exon 28402585 28404585 . + . transcript_id "LOC_Os06g46770.3"; gene_id "LOC_Os06g46770"; gene_name "LOC_Os06g46770";
Chr6 MSU_osa1r7 exon 28403718 28404585 . + . transcript_id "LOC_Os06g46770.3"; gene_id "LOC_Os06g46770"; gene_name "LOC_Os06g46770";

As you can see now the coordinates of exon2 and exon3 are wrong, they have the same end point.

Hi

I have run cufflinks on the same bamfile, twice with an important difference:

• once with the --GTF option, a normal run (below cufflinks folder),
• and once with the --GTF-guide, a novel-transcript detection run (below: cufflinks_noguide folder)

$ grep -P "TP53\t"  */isoform*
cufflinks/isoforms.fpkm_tracking:ENST00000413465    -   -   CUFF.30922  TP53    -   17:7565096-7579912  1018    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000359597    -   -   CUFF.30922  TP53    -   17:7569403-7579912  1152    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000504937    -   -   CUFF.30922  TP53    -   17:7571719-7578811  2271    83.4765 13.1751 13.1751 13.1751 OK
cufflinks/isoforms.fpkm_tracking:ENST00000504290    -   -   CUFF.30922  TP53    -   17:7571719-7578811  2331    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000510385    -   -   CUFF.30922  TP53    -   17:7571719-7578811  2404    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000269305    -   -   CUFF.30922  TP53    -   17:7571719-7590856  2579    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000420246    -   -   CUFF.30922  TP53    -   17:7571721-7590799  2653    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000455263    -   -   CUFF.30922  TP53    -   17:7571721-7590799  2580    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000445888    -   -   CUFF.30922  TP53    -   17:7571738-7590805  2506    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000576024    -   -   CUFF.30922  TP53    -   17:7572886-7576905  175 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000509690    -   -   CUFF.30922  TP53    -   17:7576852-7590805  729 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000514944    -   -   CUFF.30922  TP53    -   17:7577534-7590745  546 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000574684    -   -   CUFF.30922  TP53    -   17:7577571-7578437  104 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000505014    -   -   CUFF.30922  TP53    -   17:7577843-7590805  1261    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000508793    -   -   CUFF.30922  TP53    -   17:7578433-7580752  634 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000604348    -   -   CUFF.30922  TP53    -   17:7578479-7590805  568 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000503591    -   -   CUFF.30922  TP53    -   17:7578546-7590745  565 0   0   0   0   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000413465    -   -   ENSG00000141510 TP53    -   17:7565096-7579912  1018    0   0   0   0.0784283   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000359597    -   -   ENSG00000141510 TP53    -   17:7569403-7579912  1152    0   0   0   0.0710096   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000504937    -   -   ENSG00000141510 TP53    -   17:7571719-7578811  2271    57.4473 9.06728 8.17987 9.95469 OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000504290    -   -   ENSG00000141510 TP53    -   17:7571719-7578811  2331    8.29612e-12 1.30943e-12 0   0.0285236   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000510385    -   -   ENSG00000141510 TP53    -   17:7571719-7578811  2404    2.06479 0.325899    0.140638    0.511161    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000269305    -   -   ENSG00000141510 TP53    -   17:7571719-7590856  2579    6.32227 0.997886    0.692799    1.30297 OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000455263    -   -   ENSG00000141510 TP53    -   17:7571721-7590799  2580    4.16124e-14 6.56796e-15 0   0.0260571   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000420246    -   -   ENSG00000141510 TP53    -   17:7571721-7590799  2653    0.00293471  0.000463204 0   0.0255082   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000445888    -   -   ENSG00000141510 TP53    -   17:7571738-7590805  2506    4.00765 0.632554    0.384194    0.880913    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000576024    -   -   ENSG00000141510 TP53    -   17:7572886-7576905  175 0   0   0   0.363874    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000509690    -   -   ENSG00000141510 TP53    -   17:7576852-7590805  729 0   0   0   0.127829    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000514944    -   -   ENSG00000141510 TP53    -   17:7577534-7590745  546 0   0   0   0.187486    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000574684    -   -   ENSG00000141510 TP53    -   17:7577571-7578437  104 0   0   0   0.612288    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000505014    -   -   ENSG00000141510 TP53    -   17:7577843-7590805  1261    0   0   0   0.0624882   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000508793    -   -   ENSG00000141510 TP53    -   17:7578433-7580752  634 2.78604e-89 4.39738e-90 0   0.153351    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000604348    -   -   ENSG00000141510 TP53    -   17:7578479-7590805  568 0   0   0   0.166118    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000503591    -   -   ENSG00000141510 TP53    -   17:7578546-7590745  565 0   0   0   0.167144    OK

When I look at a known transcript in the GTF-guide run, I observe that many isoforms are missing that were reported with an FPKM value when with the normal run.

I'd think there is something wrong with one of the results - or is there an explanation for it?

Hi,

I would like to know what is the estimated runtime for RABT algorithm in a human transcriptome with around 50M paired-end reads, running with 24 threads (Intel(R) Xeon(R) CPU E5645 @ 2.40GHz). Right now I'm running cufflinks (RABT) without fragment bias or multiple reads correction and the process lasts more than 3 days!!! I need to process more than 100 samples and with this runtime will last forever...

Is it normal? am I doing something wrong?

Thanks in advance.

gffread -h command used to provide help commands, but it seems like the 2.2.1 that comes with cufflinks displays a number of messages and dumps the core. I don't know if this is expected behavior or not, so just wanted to check up on that.

The Message given shown below

*** buffer overflow detected ***: gffread terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x73f1f)[0x7f9ee9911f1f]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f9ee99a982c]
/lib/x86_64-linux-gnu/libc.so.6(+0x10a6f0)[0x7f9ee99a86f0]
/lib/x86_64-linux-gnu/libc.so.6(+0x109bf9)[0x7f9ee99a7bf9]
/lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0xbc)[0x7f9ee991a29c]
/lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0x1cd5)[0x7f9ee98e99c5]
/lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x84)[0x7f9ee99a7c84]
gffread[0x40c07c]
gffread[0x40177a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f9ee98bfec5]
gffread[0x403945]
======= Memory map: ========
00400000-0043b000 r-xp 00000000 fc:00 4995279                            /home/gokul/bin/gffread
0063a000-0063b000 r--p 0003a000 fc:00 4995279                            /home/gokul/bin/gffread
0063b000-0063c000 rw-p 0003b000 fc:00 4995279                            /home/gokul/bin/gffread
0063c000-00644000 rw-p 00000000 00:00 0 
02394000-023b5000 rw-p 00000000 00:00 0                                  [heap]
7f9ee9598000-7f9ee969d000 r-xp 00000000 fc:00 1704551                    /lib/x86_64-linux-gnu/libm-2.19.so
7f9ee969d000-7f9ee989c000 ---p 00105000 fc:00 1704551                    /lib/x86_64-linux-gnu/libm-2.19.so
7f9ee989c000-7f9ee989d000 r--p 00104000 fc:00 1704551                    /lib/x86_64-linux-gnu/libm-2.19.so
7f9ee989d000-7f9ee989e000 rw-p 00105000 fc:00 1704551                    /lib/x86_64-linux-gnu/libm-2.19.so
7f9ee989e000-7f9ee9a59000 r-xp 00000000 fc:00 1704543                    /lib/x86_64-linux-gnu/libc-2.19.so
7f9ee9a59000-7f9ee9c59000 ---p 001bb000 fc:00 1704543                    /lib/x86_64-linux-gnu/libc-2.19.so
7f9ee9c59000-7f9ee9c5d000 r--p 001bb000 fc:00 1704543                    /lib/x86_64-linux-gnu/libc-2.19.so
7f9ee9c5d000-7f9ee9c5f000 rw-p 001bf000 fc:00 1704543                    /lib/x86_64-linux-gnu/libc-2.19.so
7f9ee9c5f000-7f9ee9c64000 rw-p 00000000 00:00 0 
7f9ee9c64000-7f9ee9c7d000 r-xp 00000000 fc:00 1707887                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7f9ee9c7d000-7f9ee9e7c000 ---p 00019000 fc:00 1707887                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7f9ee9e7c000-7f9ee9e7d000 r--p 00018000 fc:00 1707887                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7f9ee9e7d000-7f9ee9e7e000 rw-p 00019000 fc:00 1707887                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7f9ee9e7e000-7f9ee9e82000 rw-p 00000000 00:00 0 
7f9ee9e82000-7f9ee9e98000 r-xp 00000000 fc:00 1716590                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f9ee9e98000-7f9eea097000 ---p 00016000 fc:00 1716590                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f9eea097000-7f9eea098000 rw-p 00015000 fc:00 1716590                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f9eea098000-7f9eea17e000 r-xp 00000000 fc:00 1975493                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f9eea17e000-7f9eea37d000 ---p 000e6000 fc:00 1975493                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f9eea37d000-7f9eea385000 r--p 000e5000 fc:00 1975493                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f9eea385000-7f9eea387000 rw-p 000ed000 fc:00 1975493                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f9eea387000-7f9eea39c000 rw-p 00000000 00:00 0 
7f9eea39c000-7f9eea3bf000 r-xp 00000000 fc:00 1704541                    /lib/x86_64-linux-gnu/ld-2.19.so
7f9eea594000-7f9eea59a000 rw-p 00000000 00:00 0 
7f9eea5bb000-7f9eea5be000 rw-p 00000000 00:00 0 
7f9eea5be000-7f9eea5bf000 r--p 00022000 fc:00 1704541                    /lib/x86_64-linux-gnu/ld-2.19.so
7f9eea5bf000-7f9eea5c0000 rw-p 00023000 fc:00 1704541                    /lib/x86_64-linux-gnu/ld-2.19.so
7f9eea5c0000-7f9eea5c1000 rw-p 00000000 00:00 0 
7fff55a3f000-7fff55a61000 rw-p 00000000 00:00 0                          [stack]
7fff55b65000-7fff55b67000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

Hi,
The README file says that pre-compiled banaries are available.
Where are they located ?

Thanks,
Alex

Hi,
I followed the instructions and downloaded samtools and installed bam headers and libbam
under /usr/local.
./configure still fails with the follwing error

checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.

Thanks,
Alex

A user sent this trace, for example:

cuffnorm -p 15 -o $cn_out/$gtf_nm --library-norm-method classic-fpkm --use-sample-sheet $gtf_file .cn_${gtf_nm}.list 2> $cn_out/$gtf_nm/my.log

*** glibc detected *** cuffnorm: free(): invalid next size (fast): 0x0000000000dab200 ***
======= Backtrace: =========
/lib64/libc.so.6[0x35f7a76166]
/lib64/libc.so.6[0x35f7a78ca3]
cuffnorm[0x4d79e1]
cuffnorm[0x417a3e]
cuffnorm[0x41abeb]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x35f7a1ed1d]
cuffnorm[0x40fe19]
======= Memory map: ========
00400000-005c3000 r-xp 00000000 4f9:2c566 144129331671661695
/lustre/tools_centos6.3/build/cufflinks-2.2.1/install/bin/cuffnorm
007c3000-007c5000 rw-p 001c3000 4f9:2c566 144129331671661695
/lustre/tools_centos6.3/build/cufflinks-2.2.1/install/bin/cuffnorm
007c5000-007d2000 rw-p 00000000 00:00 0
00d5c000-00e22000 rw-p 00000000 00:00 0 [heap]
35f7600000-35f7620000 r-xp 00000000 fd:00 1183199 /lib64/ld-2.12.so
35f781f000-35f7820000 r--p 0001f000 fd:00 1183199 /lib64/ld-2.12.so
35f7820000-35f7821000 rw-p 00020000 fd:00 1183199 /lib64/ld-2.12.so

We run cuffquant on a gzipped annotation file and it failed without any notice, just stopped. It may be helpful to throw an error that reading the annotation file did not work.

cuffdiff built from the current master segfaults when run as follows

cuffdiff -p 4 -L ctrl,siCTCF -u ./merged_LNC_CTCF_CTRL/merged.gtf LNC_ctrl_output/accepted_hits.bam LNC_siCTCF_output/accepted_hits.bam -o cuffdiff_LNC_CTCF_CTRL

GDB backtrace:

(gdb) bt
#0 0x0000003926832625 in raise () from /lib64/libc.so.6
#1 0x0000003926833e05 in abort () from /lib64/libc.so.6
#2 0x0000003926870537 in __libc_message () from /lib64/libc.so.6
#3 0x0000003926875e66 in malloc_printerr () from /lib64/libc.so.6
#4 0x0000003926879caa in _int_malloc () from /lib64/libc.so.6
#5 0x000000392687a6b1 in malloc () from /lib64/libc.so.6
#6 0x00000039294bd0bd in operator new(unsigned long) () from /usr/lib64/libstdc++.so.6
#7 0x0000000000413d4f in quantitate_next_locus (rt=..., bundle_factories=..., launcher=...) at cuffdiff.cpp:965
#8 0x000000000041accc in driver (ref_gtf=0x82d0a0, mask_gtf=0x6dd, contrast_file=0x7ffffffebc78, norm_standards_file=0xa340000000000000, sam_hit_filename_lists=..., outfiles=...) at cuffdiff.cpp:1831
#9 0x000000000041f081 in main (argc=, argv=0x82a570) at cuffdiff.cpp:2684

Processing Locus chr1:109656584-109749403 [* ] 4%[New Thread 0x2aaaabf80700 (LWP 12356)]
Processing Locus chr1:110292701-110306644 [* ] 4%[Thread 0x2aaaabf80700 (LWP 12356) exited]
Processing Locus chr1:182023704-182030847 [* ] 7%[New Thread 0x2aaaabf80700 (LWP 12357)]
Processing Locus chr1:183605207-183897666 [* ] 7%[Thread 0x2aaaabf80700 (LWP 12357) exited]
Processing Locus chr1:209929393-209957890 [** ] 8%*** glibc detected *** /apps/tuxedo/cufflinks/2.2.2/bin/cuffdiff: corrupted double-linked list: 0x000000000486ce90 ***

Valgrind memcheck:

valgrind --leak-check=yes cuffdiff -p 8 -L ctrl,siCTCF -u ./merged_LNC_CTCF_CTRL/merged.gtf LNC_ctrl_output/accepted_hits.bam LNC_siCTCF_output/accepted_hits.bam -o cuffdiff_LNC_CTCF_CTRL
==18491== Memcheck, a memory error detector
==18491== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al.
==18491== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright info
==18491== Command: cuffdiff -p 8 -L ctrl,siCTCF -u ./merged_LNC_CTCF_CTRL/merged.gtf LNC_ctrl_output/accepted_hits.bam LNC_siCTCF_output/accepted_hits.bam -o cuffdiff_LNC_CTCF_CTRL
==18491==
You are using Cufflinks v2.2.2, which is the most recent release.
[15:50:22] Loading reference annotation.
Warning: No conditions are replicated, switching to 'blind' dispersion method
[15:52:02] Inspecting maps and determining fragment length distributions.
[15:54:43] Modeling fragment count overdispersion.

Warning: compparcomp: perfect fit
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Warning: procv: no points with non-zero weight
Error: attempting to re-initialize still-live variable _lfwork
Error: attempting to re-initialize still-live variable _lfiwork
==18491== Invalid write of size 8
==18491== at 0x4A09D13: memcpy (mc_replace_strmem.c:882)
==18491== by 0x52BB2E: reassign (ev_main.c:135)
==18491== by 0x52BDA0: newsplit (ev_main.c:264)
==18491== by 0x528023: atree_grow.clone.0 (ev_atree.c:117)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== Address 0x1529d5d0 is 0 bytes after a block of size 3,488 alloc'd
==18491== at 0x4A0677B: calloc (vg_replace_malloc.c:593)
==18491== by 0x513053: createvar (vari.cpp:295)
==18491== by 0x52B59D: trchck (ev_main.c:89)
==18491== by 0x52BA96: reassign (ev_main.c:126)
==18491== by 0x52BDA0: newsplit (ev_main.c:264)
==18491== by 0x528023: atree_grow.clone.0 (ev_atree.c:117)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== Address 0x62f7e88 is 8 bytes before a block of size 152 alloc'd
==18491== at 0x4A085BC: operator new(unsigned long) (vg_replace_malloc.c:298)
==18491== by 0x4A3FE8: load_ref_rnas(IO_FILE, RefSequenceTable&, std::vectorboost::shared_ptr<Scaffold, std::allocatorboost::shared_ptr >&, boost::crc_optimal<32ul, 79764919u, 4294967295u, 4294967295u, true, true>&, bool, bool) (bundles.cpp:228)
==18491== by 0x418603: driver(IO_FILE, IO_FILE, IO_FILE, IO_FILE, std::vector<std::string, std::allocatorstd::string >&, Outfiles&) (cuffdiff.cpp:1637)
==18491== by 0x41F080: main (cuffdiff.cpp:2684)
==18491==
==18491== Invalid read of size 8
==18491== at 0x4A09D0C: memcpy (mc_replace_strmem.c:882)
==18491== by 0x52BB63: reassign (ev_main.c:138)
==18491== by 0x52BDA0: newsplit (ev_main.c:264)
==18491== by 0x528023: atree_grow.clone.0 (ev_atree.c:117)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== Address 0x62f8050 is not stack'd, malloc'd or (recently) free'd
==18491==
Error: attempting to re-initialize still-live variable _lfwork
Error: attempting to re-initialize still-live variable lfiwork
==18491== Invalid read of size 8
==18491== at 0x4A09BFE: memcpy (mc_replace_strmem.c:882)
==18491== by 0x52BB2E: reassign (ev_main.c:135)
==18491== by 0x52BDA0: newsplit (ev_main.c:264)
==18491== by 0x528023: atree_grow.clone.0 (ev_atree.c:117)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x5283AA: atree_start (ev_atree.c:163)
==18491== by 0x5103D8: startlf.clone.0 (startlf.c:215)
==18491== by 0x511CCB: clocfit (startlf.c:432)
==18491== by 0x4F181B: cmdint (cmd.c:696)
==18491== by 0x4F18F9: locfit_dispatch (cmd.c:748)
==18491== by 0x4E12D4: fit_dispersion_model_helper(std::string const&, std::vector<double, std::allocator > const&, std::vector<LocusCountList, std::allocator > const&) (replicates.cpp:825)
==18491== Address 0x1529d5d0 is 0 bytes after a block of size 3,488 alloc'd
==18491== at 0x4A0677B: calloc (vg_replace_malloc.c:593)
==18491== by 0x513053: createvar (vari.cpp:295)
==18491== by 0x52B59D: trchck (ev_main.c:89)
==18491== by 0x52BA96: reassign (ev_main.c:126)
==18491== by 0x52BDA0: newsplit (ev_main.c:264)
==18491== by 0x528023: atree_grow.clone.0 (ev_atree.c:117)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491== by 0x52810A: atree_grow.clone.0 (ev_atree.c:122)
==18491==
==18491== Invalid write of size 8
==18491== at 0x4A09BF3: memcpy (mc_replace_strmem.c:882)
==18491== by 0x52BB2E: reassign (ev_main.c:135)
==18491== by 0x52BDA0: newsplit (ev_main.c:264)
==18491== by 0x528023: atree_grow.clone.0 (ev_atree.c:117)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x5283AA: atree_start (ev_atree.c:163)
==18491== by 0x5103D8: startlf.clone.0 (startlf.c:215)
==18491== by 0x511CCB: clocfit (startlf.c:432)
==18491== by 0x4F181B: cmdint (cmd.c:696)
==18491== by 0x4F18F9: locfit_dispatch (cmd.c:748)
==18491== by 0x4E12D4: fit_dispersion_model_helper(std::string const&, std::vector<double, std::allocator > const&, std::vector<LocusCountList, std::allocator > const&) (replicates.cpp:825)
==18491== Address 0x7074710 is 0 bytes after a block of size 6,832 alloc'd
==18491== at 0x4A0677B: calloc (vg_replace_malloc.c:593)
==18491== by 0x513053: createvar (vari.cpp:295)
==18491== by 0x52B59D: trchck (ev_main.c:89)
==18491== by 0x52BA96: reassign (ev_main.c:126)
==18491== by 0x52BDA0: newsplit (ev_main.c:264)
==18491== by 0x528023: atree_grow.clone.0 (ev_atree.c:117)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x5283AA: atree_start (ev_atree.c:163)
==18491== by 0x5103D8: startlf.clone.0 (startlf.c:215)
==18491== by 0x511CCB: clocfit (startlf.c:432)
==18491== by 0x4F181B: cmdint (cmd.c:696)
==18491==
==18491== Invalid read of size 8
==18491== at 0x4A09BE8: memcpy (mc_replace_strmem.c:882)
==18491== by 0x52BB2E: reassign (ev_main.c:135)
==18491== by 0x52BDA0: newsplit (ev_main.c:264)
==18491== by 0x528023: atree_grow.clone.0 (ev_atree.c:117)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x5283AA: atree_start (ev_atree.c:163)
==18491== by 0x5103D8: startlf.clone.0 (startlf.c:215)
==18491== by 0x511CCB: clocfit (startlf.c:432)
==18491== by 0x4F181B: cmdint (cmd.c:696)
==18491== by 0x4F18F9: locfit_dispatch (cmd.c:748)
==18491== by 0x4E12D4: fit_dispersion_model_helper(std::string const&, std::vector<double, std::allocator > const&, std::vector<LocusCountList, std::allocator > const&) (replicates.cpp:825)
==18491== Address 0x1529d5e8 is not stack'd, malloc'd or (recently) free'd
==18491==
==18491== Invalid read of size 8
==18491== at 0x4A09BE8: memcpy (mc_replace_strmem.c:882)
==18491== by 0x52BB63: reassign (ev_main.c:138)
==18491== by 0x52BDA0: newsplit (ev_main.c:264)
==18491== by 0x528023: atree_grow.clone.0 (ev_atree.c:117)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x5283AA: atree_start (ev_atree.c:163)
==18491== by 0x5103D8: startlf.clone.0 (startlf.c:215)
==18491== by 0x511CCB: clocfit (startlf.c:432)
==18491== by 0x4F181B: cmdint (cmd.c:696)
==18491== by 0x4F18F9: locfit_dispatch (cmd.c:748)
==18491== by 0x4E12D4: fit_dispersion_model_helper(std::string const&, std::vector<double, std::allocator > const&, std::vector<LocusCountList, std::allocator > const&) (replicates.cpp:825)
==18491== Address 0x1529da00 is 16 bytes before a block of size 16 alloc'd
==18491== at 0x4A085BC: operator new(unsigned long) (vg_replace_malloc.c:298)
==18491== by 0x428FBE: std::vector<std::string, std::allocatorstd::string >::vector(std::vector<std::string, std::allocatorstd::string > const&) (new_allocator.h:89)
==18491== by 0x429375: LocusCount std::__uninitialized_copy_a<__gnu_cxx::_normal_iterator<LocusCount const*, std::vector<LocusCount, std::allocator > >, LocusCount, LocusCount>(__gnu_cxx::_normal_iterator<LocusCount const, std::vector<LocusCount, std::allocator > >, __gnu_cxx::normal_iterator<LocusCount const*, std::vector<LocusCount, std::allocator > >, LocusCount, std::allocator&) (common.h:378)
==18491== by 0x42C9DB: std::vector<LocusCount, std::allocator >::operator=(std::vector<LocusCount, std::allocator > const&) (stl_vector.h:966)
==18491== by 0x4E34BB: normalize_counts(std::vectorboost::shared_ptr<ReadGroupProperties, std::allocatorboost::shared_ptr >&) (common.h:598)
==18491== by 0x41A2EA: driver(IO_FILE, IO_FILE, IO_FILE, IO_FILE, std::vector<std::string, std::allocatorstd::string >&, Outfiles&) (cuffdiff.cpp:1765)
==18491== by 0x41F080: main (cuffdiff.cpp:2684)
==18491==
==18491== Invalid read of size 8
==18491== at 0x4A09BFE: memcpy (mc_replace_strmem.c:882)
==18491== by 0x52BB63: reassign (ev_main.c:138)
==18491== by 0x52BDA0: newsplit (ev_main.c:264)
==18491== by 0x528023: atree_grow.clone.0 (ev_atree.c:117)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x528073: atree_grow.clone.0 (ev_atree.c:128)
==18491== by 0x5283AA: atree_start (ev_atree.c:163)
==18491== by 0x5103D8: startlf.clone.0 (startlf.c:215)
==18491== by 0x511CCB: clocfit (startlf.c:432)
==18491== by 0x4F181B: cmdint (cmd.c:696)
==18491== by 0x4F18F9: locfit_dispatch (cmd.c:748)
==18491== by 0x4E12D4: fit_dispersion_model_helper(std::string const&, std::vector<double, std::allocator > const&, std::vector<LocusCountList, std::allocator > const&) (replicates.cpp:825)
==18491== Address 0x1529da20 is 0 bytes after a block of size 16 alloc'd
==18491== at 0x4A085BC: operator new(unsigned long) (vg_replace_malloc.c:298)
==18491== by 0x428FBE: std::vector<std::string, std::allocatorstd::string >::vector(std::vector<std::string, std::allocatorstd::string > const&) (new_allocator.h:89)
==18491== by 0x429375: LocusCount std::__uninitialized_copy_a<__gnu_cxx::_normal_iterator<LocusCount const*, std::vector<LocusCount, std::allocator > >, LocusCount, LocusCount>(__gnu_cxx::_normal_iterator<LocusCount const, std::vector<LocusCount, std::allocator > >, __gnu_cxx::_normal_iterator<LocusCount const*, std::vector<LocusCount, std::allocator > >, LocusCount, std::allocator&) (common.h:378)
==18491== by 0x42C9DB: std::vector<LocusCount, std::allocator >::operator=(std::vector<LocusCount, std::allocator > const&) (stl_vector.h:966)
==18491== by 0x4E34BB: normalize_counts(std::vectorboost::shared_ptr<ReadGroupProperties, std::allocatorboost::shared_ptr >&) (common.h:598)
==18491== by 0x41A2EA: driver(IO_FILE, IO_FILE, IO_FILE, _IO_FILE*, std::vector<std::string, std::allocatorstd::string >&, Outfiles&) (cuffdiff.cpp:1765)
==18491== by 0x41F080: main (cuffdiff.cpp:2684)
==18491==

Map Properties:

  Normalized Map Mass: 25.50
  Raw Map Mass: 26.00
  Number of Multi-Reads: 74 (with 148 total hits)
  Fragment Length Distribution: Truncated Gaussian (default)
                Default Mean: 200
             Default Std Dev: 80

Map Properties:
Normalized Map Mass: 25.50
Raw Map Mass: 27.00
Number of Multi-Reads: 70 (with 139 total hits)
Fragment Length Distribution: Truncated Gaussian (default)
Default Mean: 200
Default Std Dev: 80
[17:06:46] Calculating preliminary abundance estimates
Processing Locus chr1:70820492-70833705 [ ] 3%
valgrind: m_mallocfree.c:294 (get_bszB_as_is): Assertion 'bszB_lo == bszB_hi' failed.
valgrind: Heap block lo/hi size mismatch: lo = 80, hi = 1888.
This is probably caused by your program erroneously writing past the
end of a heap block and corrupting heap metadata. If you fix any
invalid writes reported by Memcheck, this assertion failure will
probably go away. Please try that before reporting this as a bug.

==18491== at 0x38031DA7: report_and_quit (m_libcassert.c:235)
==18491== by 0x38031FE0: vgPlain_assert_fail (m_libcassert.c:309)
==18491== by 0x3803CBBD: get_bszB (m_mallocfree.c:294)
==18491== by 0x3803E86E: vgPlain_arena_free (m_mallocfree.c:1810)
==18491== by 0x38003667: create_MC_Chunk (mc_malloc_wrappers.c:165)
==18491== by 0x38003BE0: vgMemCheck_new_block (mc_malloc_wrappers.c:283)
==18491== by 0x3800409A: vgMemCheck_malloc (mc_malloc_wrappers.c:301)
==18491== by 0x3807A58A: vgPlain_scheduler (scheduler.c:1665)
==18491== by 0x380A5A19: run_a_thread_NORETURN (syswrap-linux.c:103)

sched status:
running_tid=1

Thread 1: status = VgTs_Runnable
==18491== at 0x4A079EE: malloc (vg_replace_malloc.c:270)
==18491== by 0x4A07B62: realloc (vg_replace_malloc.c:662)
==18491== by 0x561236: bam_read1 (sam.c:350)
==18491== by 0x567B0D: sam_read1 (sam.c:916)
==18491== by 0x49A27A: BAMHitFactory::next_record(char const_&, unsigned long&) (sam.h:95)
==18491== by 0x4A1EDF: BundleFactory::next_valid_alignment(ReadHit const_&) (bundles.cpp:673)
==18491== by 0x4AD8BA: BundleFactory::next_bundle_ref_driven(HitBundle&) (bundles.cpp:910)
==18491== by 0x4AE2B1: BundleFactory::next_bundle(HitBundle&, bool) (bundles.cpp:1168)
==18491== by 0x4330EC: ReplicatedBundleFactory::next_bundle(HitBundle&, bool) (replicates.h:190)
==18491== by 0x4142A9: quantitate_next_locus(RefSequenceTable const&, std::vectorboost::shared_ptr<ReplicatedBundleFactory, std::allocatorboost::shared_ptr >&, boost::shared_ptr) (cuffdiff.cpp:986)
==18491== by 0x41ACCB: driver(IO_FILE, IO_FILE, IO_FILE, IO_FILE, std::vector<std::string, std::allocatorstd::string >&, Outfiles&) (cuffdiff.cpp:1831)
==18491== by 0x41F080: main (cuffdiff.cpp:2684)

We are using cufflinks on an HPC system with the main project space on a lustre filesystem. We noticed cufflinks routinely failing for users when they specified an absolute path for an output directory with -o

On further investigation it appears that the mkpath funtion in src/common.cpp is recursive and calling mkdir at each level of the requested path, from root to tip. If a level exists it expects, and handles, an EEXIST error from mkdir.

Unfortunately lustre can return EPERM for mkdir against an existing directory:

https://jira.hpdd.intel.com/browse/LU-4185

This is a long-standing issue with lustre, which doesn't appear to be going away. We don't hit it in other software that does recursive directory creation as they generally call stat to find how much of the structure exists, rather than relying on EEXIST being returned from mkdir.

I will patch cufflinks locally for this issue, to use stat in this manner. Would this be considered as a PR?

It would really be useful for those of us that prefer to pull from github and build locally if release commits were tagged.

I used cuffcompare (v 2.2.1) to compare two sets of trasnctipts.

cuffcompare -r $ref_gtf -s $genome -o $OUT A.gtf B.gtf

But I found the row number of result XXX.tracking is less than the number of transcript numbers in $ref_gtf, is some transcripts lost due to some reasons?

From Chris Smowton:

Just debugged a segfault that resulted from a SAM file that alleged to be aligned (flags & 4 == 0), but which had the CIGAR string “76I”. That leads to a Scaffold with zero-length aug_ops, and a null pointer deref when you try Scaffold::left(). The record is nonsensical (what does it mean to have a coordinate but zero concurrence with the genome at that coordinate?) but found in the wild (TCGA dataset).

I suggest that either the SAM parser or the Hit->Scaffold code should check for either all-INS or zero-aug-ops case and discard the record / print a clear warning in this case.

I first posted this problem on the cufflinks mailing list but no replies yet ( https://groups.google.com/forum/#!topic/tuxedo-tools-users/_E94jkdvMak )

The problem we are experiencing is that in GRCH38 annotation from refseq the gene HLA-B is annotated on chromosome 6 and in between its exons 4,5 there is an MiRNA annotated called MIR6891. The quantification with Cuffquant goes terribly wrong here as the table below will show:

HLA-B 1340.16 994.534 923.688 1650.58 1266.27 2167.43 2692.21
MIR6891 329936 167527 113865 399491 282248 82857.6 114646

As you can see i got counts for the MIR which go through the roof while the HLA-B gene is relatively low expressed compared to the MIR. When checking in IGV or UCSC genome browser i see that there is not a single read aligning to the MIR but a lot of split reads cover the region. Our current guess is now that these split reads are all asigned to the MIR as well, while the actual bases are aligned to exon 4 and 5 of the HLA-B gene. I know this is probably not easy to fix, but maybe a good idea to distribute a GTF file containing only MRNAs and LINCRNA. Or something like that, i wonder if other users experienced the same issue and how they circumvented the issue. Thanks already!

./configure output:

user@user-HP:~/Downloads/bioinformatics/cufflinks-master$ ./configure --with-eigen=/usr/local/include/Eigen --with-boost=/home/user/Downloads/boost_1_55
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for ar... ar
checking the archiver (ar) interface... ar
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/dist-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages
checking for boostlib >= 1.47.0... yes
checking for bamlib... yes
checking build system type... x86_64-unknown-linux-gnu
checking whether the Boost::System library is available... no
checking whether the Boost::Serialization library is available... no
checking whether the Boost::Thread library is available... no
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
checking for eigenlib... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for ptrdiff_t... yes
checking host system type... x86_64-unknown-linux-gnu
checking if gcc accepts -m64... yes
checking for struct sysinfo.totalram... yes
checking whether sysctl is declared... yes
checking whether CTL_HW is declared... no
checking whether HW_PHYSMEM is declared... no
checking how to create a pax tar archive... gnutar
checking dependency style of gcc... (cached) gcc3
checking dependency style of g++... (cached) gcc3
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands

-- cufflinks 2.2.1 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -DNDEBUG -I/home/user/Downloads/boost_1_55/include -I/usr/local/include -I/usr/local/include/Eigen/include
GCC version: gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2
Host System type: x86_64-unknown-linux-gnu
Install prefix: /usr/local
Install eprefix: ${prefix}

See config.h for further configuration information.
Email [email protected] with questions and bug reports.

-- cufflinks 2.2.1 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -DNDEBUG -pthread -I/usr/include -I/usr/local/include
GCC version: gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2
Host System type: x86_64-unknown-linux-gnu
Install prefix: /usr/local
Install eprefix: ${prefix}

See config.h for further configuration information.
Email [email protected] with questions and bug reports.

make output:

user@user-HP:~/Downloads/bioinformatics/cufflinks-master$ make
make all-recursive
make[1]: Entering directory /home/user/Downloads/bioinformatics/cufflinks-master' Making all in src make[2]: Entering directory/home/user/Downloads/bioinformatics/cufflinks-master/src'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -DNDEBUG -pthread -I/home/user/Downloads/boost_1_55/include -I/usr/local/include -I/usr/local/include/Eigen/include -MT abundances.o -MD -MP -MF .deps/abundances.Tpo -c -o abundances.o abundances.cpp
In file included from ../boost/numeric/ublas/matrix.hpp:20:0,
from abundances.h:18,
from abundances.cpp:16:
../boost/numeric/ublas/detail/matrix_assign.hpp: In function ‘void boost::numeric::ublas::matrix_swap(M&, boost::numeric::ublas::matrix_expression&, boost::numeric::ublas::dense_proxy_tag, boost::numeric::ublas::row_major_tag)’:
../boost/numeric/ublas/detail/matrix_assign.hpp:1262:39: warning: typedef ‘size_type’ locally defined but not used [-Wunused-local-typedefs]
typedef typename M::size_type size_type;
^
../boost/numeric/ublas/detail/matrix_assign.hpp: In function ‘void boost::numeric::ublas::matrix_swap(M&, boost::numeric::ublas::matrix_expression&, boost::numeric::ublas::dense_proxy_tag, boost::numeric::ublas::column_major_tag)’:
../boost/numeric/ublas/detail/matrix_assign.hpp:1288:39: warning: typedef ‘size_type’ locally defined but not used [-Wunused-local-typedefs]
typedef typename M::size_type size_type;
^
In file included from abundances.h:23:0,
from abundances.cpp:16:
hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’:
hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder]
std::ifstream _ifs;
^
In file included from abundances.h:23:0,
from abundances.cpp:16:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from abundances.cpp:43:0:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’:
replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable]
const vectorboost::shared_ptr& s2 = bundles[i-1]->ref_scaffolds();
^
In file included from abundances.cpp:44:0:
sampling.h: In function ‘double boost::numeric::ublas::cholesky_factorize(M&)’:
sampling.h:50:13: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef M matrix_type;
^
In file included from abundances.cpp:44:0:
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression&)’:
sampling.h:113:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:114:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs]
typedef vector vector_type;
^
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression&)’:
sampling.h:120:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:121:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef matrix matrix_type;
^
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression&, const M&)’:
sampling.h:127:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:128:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs]
typedef vector vector_type;
^
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression&, const M&)’:
sampling.h:134:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:135:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef matrix matrix_type;
^
abundances.cpp: In constructor ‘AbundanceGroup::AbundanceGroup(const std::vectorboost::shared_ptr&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const std::set<boost::shared_ptr >&)’:
abundances.cpp:518:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test)
^
abundances.cpp: In member function ‘virtual AbundanceStatus AbundanceGroup::status() const’:
abundances.cpp:526:10: warning: variable ‘has_lowdata_member’ set but not used [-Wunused-but-set-variable]
bool has_lowdata_member = false;
^
abundances.cpp: In member function ‘void AbundanceGroup::collect_per_replicate_mass(const std::vector&, std::vectorboost::shared_ptr&)’:
abundances.cpp:1043:20: warning: unused variable ‘curr_mass’ [-Wunused-variable]
double curr_mass = inserted.first->second;
^
abundances.cpp: In function ‘void collapse_equivalent_hits(const std::vector&, std::vectorboost::shared_ptr&, std::vector&, std::vector&, bool)’:
abundances.cpp:1160:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < N; ++j)
^
abundances.cpp:1347:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < nr_alignments.size(); ++i)
^
abundances.cpp: In function ‘AbundanceStatus bootstrap_gamma_mle(const std::vectorboost::shared_ptr&, const std::vector&, const std::vector&, boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator > >&, boost::numeric::ublas::matrix&, double&)’:
abundances.cpp:1488:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < num_bootstrap_samples; ++i)
^
abundances.cpp:1491:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < num_sample_frags; ++j)
^
abundances.cpp:1505:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
sample_idxs[curr_sample] >= processed_hits &&
^
abundances.cpp: In function ‘bool generate_count_assignment_samples(int, const std::vector&, const boost::numeric::ublas::matrix&, std::vector<boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator > > >&)’:
abundances.cpp:1693:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t assign_idx = 0; assign_idx < num_draws; ++assign_idx)
^
abundances.cpp: In function ‘void calculate_gamma_mle_covariance(const std::map<boost::shared_ptr, boost::shared_ptr >&, boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator > >&, boost::numeric::ublas::matrix&)’:
abundances.cpp:1760:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < all_assigned_count_samples[i].size(); ++j)
^
abundances.cpp:1775:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < num_transcripts; ++i)
^
abundances.cpp:1777:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < num_transcripts; ++j)
^
abundances.cpp: In function ‘void calculate_fragment_assignment_distribution(const std::map<boost::shared_ptr, boost::shared_ptr >&, boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator > >&, boost::numeric::ublas::matrix&, std::vector<boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator > > >&)’:
abundances.cpp:1870:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < all_assigned_count_samples[i].size(); ++j)
^
abundances.cpp:1885:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < num_transcripts; ++i)
^
abundances.cpp:1887:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < num_transcripts; ++j)
^
abundances.cpp: In member function ‘void AbundanceGroup::calculate_abundance_group_variance(const std::vectorboost::shared_ptr&, const std::map<boost::shared_ptr, boost::shared_ptr >&)’:
abundances.cpp:1968:65: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test)
^
abundances.cpp: In member function ‘void AbundanceGroup::aggregate_replicate_abundances(const std::map<boost::shared_ptr, boost::shared_ptr >&)’:
abundances.cpp:2070:58: warning: unused variable ‘sc_ab’ [-Wunused-variable]
const vectorboost::shared_ptr& sc_ab = itr->second->abundances();
^
abundances.cpp: In function ‘bool estimate_count_variance(long double&, double, double, double, double, double)’:
abundances.cpp:2277:17: warning: variable ‘bnb_mean’ set but not used [-Wunused-but-set-variable]
long double bnb_mean = 0.0;
^
abundances.cpp: In member function ‘void AbundanceGroup::generate_fpkm_samples()’:
abundances.cpp:2668:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < sample.size(); ++j)
^
abundances.cpp: In member function ‘void AbundanceGroup::calculate_FPKM_covariance()’:
abundances.cpp:2783:42: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if (length_i > 0 && length_j > 0 & M > 0)
^
abundances.cpp:2796:24: warning: unused variable ‘fpkm’ [-Wunused-variable]
double fpkm = _abundances[i]->FPKM();
^
abundances.cpp: In member function ‘void AbundanceGroup::calculate_conf_intervals()’:
abundances.cpp:2920:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < N; ++j)
^
abundances.cpp:2939:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < N; ++j)
^
abundances.cpp: In function ‘void calculate_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)’:
abundances.cpp:3352:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < alignment_multiplicities.size(); ++i)
^
abundances.cpp: In function ‘void calculate_average_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)’:
abundances.cpp:3378:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < alignment_multiplicities.size(); ++i)
^
abundances.cpp:3393:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < alignment_multiplicities.size(); ++i)
^
abundances.cpp:3395:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < proposed_gammas.size(); ++j)
^
abundances.cpp:3408:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < proposed_gammas.size(); ++j)
^
abundances.cpp: In function ‘bool is_identifiable(M&, PM&)’:
abundances.cpp:4254:15: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef M matrix_type;
^
abundances.cpp: In function ‘AbundanceStatus gamma_mle(const std::vectorboost::shared_ptr&, const std::vector&, const std::vector&, std::vector&, bool)’:
abundances.cpp:4322:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < cond_probs.rows(); ++j)
^
abundances.cpp:4324:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < cond_probs.cols(); ++i)
^
abundances.cpp:4318:10: warning: variable ‘logL’ set but not used [-Wunused-but-set-variable]
double logL;
^
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<T1, T2>::pair(const std::pair<U1, U2>&) [with U1 = const void; U2 = boost::shared_ptr; T1 = const void const; T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptr_helper::reset(SPT&, T) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/serialization.hpp:128:27: [ skipping 57 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::export_guid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
/usr/include/c++/4.8/bits/stl_pair.h:119:39: error: no matching function for call to ‘boost::shared_ptr::shared_ptr(const boost::shared_ptr&)’
: first(__p.first), second(__p.second) { }
^
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: candidates are:
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:467:14: note: template boost::shared_ptr::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type)
explicit shared_ptr( Ap r, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type = 0 ): px( r.get() ), pn()
^
../boost/smart_ptr/shared_ptr.hpp:467:14: note: template argument deduction/substitution failed:
../boost/smart_ptr/shared_ptr.hpp: In substitution of ‘template boost::shared_ptr::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type) [with Ap = boost::shared_ptr]’:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: required from ‘std::pair<T1, T2>::pair(const std::pair<U1, U2>&) [with U1 = const void; U2 = boost::shared_ptr; T1 = const void const; T2 = boost::shared_ptr]’
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptr_helper::reset(SPT&, T) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: [ skipping 58 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::export_guid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:467:14: error: no type named ‘type’ in ‘struct boost::detail::sp_enable_if_auto_ptr<boost::shared_ptr, int>’
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<T1, T2>::pair(const std::pair<U1, U2>&) [with U1 = const void; U2 = boost::shared_ptr; T1 = const void const; T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptr_helper::reset(SPT&, T) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/serialization.hpp:128:27: [ skipping 57 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::export_guid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:441:14: note: template boost::shared_ptr::shared_ptr(std::auto_ptr<_Tp1>&)
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^
../boost/smart_ptr/shared_ptr.hpp:441:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: types ‘std::auto_ptr’ and ‘const boost::shared_ptr’ have incompatible cv-qualifiers
: first(__p.first), second(_p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:434:5: note: template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, boost::shared_ptr::element_type)
shared_ptr( shared_ptr const & r, element_type * p ) BOOST_NOEXCEPT : px( p ), pn( r.pn )
^
../boost/smart_ptr/shared_ptr.hpp:434:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: candidate expects 2 arguments, 1 provided
: first(__p.first), second(__p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:420:5: note: template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, typename boost::detail::sp_enable_if_convertible<Y, T>::type)
shared_ptr( shared_ptr const & r, typename boost::detail::sp_enable_if_convertible<Y,T>::type = boost::detail::sp_empty() )
^
../boost/smart_ptr/shared_ptr.hpp:420:5: note: template argument deduction/substitution failed:
../boost/smart_ptr/shared_ptr.hpp: In substitution of ‘template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, typename boost::detail::sp_enable_if_convertible<Y, T>::type) [with Y = const ReadGroupProperties]’:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: required from ‘std::pair<_T1, T2>::pair(const std::pair<U1, U2>&) [with U1 = const void; U2 = boost::shared_ptr; T1 = const void* const; T2 = boost::shared_ptr]’
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptr_helper::reset(SPT&, T) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: [ skipping 58 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::export_guid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:420:5: error: no type named ‘type’ in ‘struct boost::detail::sp_enable_if_convertible<const ReadGroupProperties, void>’
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<T1, T2>::pair(const std::pair<U1, U2>&) [with U1 = const void; U2 = boost::shared_ptr; T1 = const void const; T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptr_helper::reset(SPT&, T) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/serialization.hpp:128:27: [ skipping 57 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::export_guid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:408:5: note: template boost::shared_ptr::shared_ptr(const boost::weak_ptr&, boost::detail::sp_nothrow_tag)
shared_ptr( weak_ptr const & r, boost::detail::sp_nothrow_tag )
^
../boost/smart_ptr/shared_ptr.hpp:408:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: ‘const boost::shared_ptr’ is not derived from ‘const boost::weak_ptr’
: first(__p.first), second(__p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:399:14: note: template boost::shared_ptr::shared_ptr(const boost::weak_ptr&)
explicit shared_ptr( weak_ptr const & r ): pn( r.pn ) // may throw
^
../boost/smart_ptr/shared_ptr.hpp:399:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: ‘const boost::shared_ptr’ is not derived from ‘const boost::weak_ptr’
: first(__p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:373:41: note: template<class Y, class D, class A> boost::shared_ptr::shared_ptr(Y, D, A)
template<class Y, class D, class A> shared_ptr( Y * p, D d, A a ): px( p ), pn( p, d, a )
^
../boost/smart_ptr/shared_ptr.hpp:373:41: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(__p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:358:32: note: template<class Y, class D> boost::shared_ptr::shared_ptr(Y, D)
template<class Y, class D> shared_ptr( Y * p, D d ): px( p ), pn( p, d )
^
../boost/smart_ptr/shared_ptr.hpp:358:32: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(__p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:347:14: note: template boost::shared_ptr::shared_ptr(Y)
explicit shared_ptr( Y * p ): px( p ), pn() // Y must be complete
^
../boost/smart_ptr/shared_ptr.hpp:347:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(__p.first), second(__p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:334:5: note: boost::shared_ptr::shared_ptr() [with T = void]
shared_ptr() BOOST_NOEXCEPT : px( 0 ), pn() // never throws in 1.30+
^
../boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate expects 0 arguments, 1 provided
../boost/smart_ptr/shared_ptr.hpp:323:25: note: boost::shared_ptr::shared_ptr(const boost::shared_ptr&)
template class shared_ptr
^
../boost/smart_ptr/shared_ptr.hpp:323:25: note: no known conversion for argument 1 from ‘const boost::shared_ptr’ to ‘const boost::shared_ptr&’
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<T1, T2>::pair(const std::pair<U1, U2>&) [with U1 = const void; U2 = boost::shared_ptr; T1 = const void const; T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptr_helper::reset(SPT&, T) [with T = const EmpDist; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/serialization.hpp:128:27: [ skipping 105 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::export_guid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
/usr/include/c++/4.8/bits/stl_pair.h:119:39: error: no matching function for call to ‘boost::shared_ptr::shared_ptr(const boost::shared_ptr&)’
: first(__p.first), second(__p.second) { }
^
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: candidates are:
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:467:14: note: template boost::shared_ptr::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type)
explicit shared_ptr( Ap r, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type = 0 ): px( r.get() ), pn()
^
../boost/smart_ptr/shared_ptr.hpp:467:14: note: template argument deduction/substitution failed:
../boost/smart_ptr/shared_ptr.hpp: In substitution of ‘template boost::shared_ptr::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type) [with Ap = boost::shared_ptr]’:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: required from ‘std::pair<T1, T2>::pair(const std::pair<U1, U2>&) [with U1 = const void; U2 = boost::shared_ptr; T1 = const void const; T2 = boost::shared_ptr]’
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptr_helper::reset(SPT&, T) [with T = const EmpDist; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: [ skipping 106 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::export_guid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:467:14: error: no type named ‘type’ in ‘struct boost::detail::sp_enable_if_auto_ptr<boost::shared_ptr, int>’
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<T1, T2>::pair(const std::pair<U1, U2>&) [with U1 = const void; U2 = boost::shared_ptr; T1 = const void const; T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptr_helper::reset(SPT&, T) [with T = const EmpDist; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/serialization.hpp:128:27: [ skipping 105 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::export_guid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:441:14: note: template boost::shared_ptr::shared_ptr(std::auto_ptr<_Tp1>&)
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^
../boost/smart_ptr/shared_ptr.hpp:441:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: types ‘std::auto_ptr’ and ‘const boost::shared_ptr’ have incompatible cv-qualifiers
: first(__p.first), second(_p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:434:5: note: template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, boost::shared_ptr::element_type)
shared_ptr( shared_ptr const & r, element_type * p ) BOOST_NOEXCEPT : px( p ), pn( r.pn )
^
../boost/smart_ptr/shared_ptr.hpp:434:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: candidate expects 2 arguments, 1 provided
: first(__p.first), second(__p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:420:5: note: template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, typename boost::detail::sp_enable_if_convertible<Y, T>::type)
shared_ptr( shared_ptr const & r, typename boost::detail::sp_enable_if_convertible<Y,T>::type = boost::detail::sp_empty() )
^
../boost/smart_ptr/shared_ptr.hpp:420:5: note: template argument deduction/substitution failed:
../boost/smart_ptr/shared_ptr.hpp: In substitution of ‘template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, typename boost::detail::sp_enable_if_convertible<Y, T>::type) [with Y = const EmpDist]’:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: required from ‘std::pair<_T1, T2>::pair(const std::pair<U1, U2>&) [with U1 = const void; U2 = boost::shared_ptr; T1 = const void* const; T2 = boost::shared_ptr]’
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptr_helper::reset(SPT&, T) [with T = const EmpDist; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: [ skipping 106 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::export_guid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:420:5: error: no type named ‘type’ in ‘struct boost::detail::sp_enable_if_convertible<const EmpDist, void>’
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<T1, T2>::pair(const std::pair<U1, U2>&) [with U1 = const void; U2 = boost::shared_ptr; T1 = const void const; T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptr_helper::reset(SPT&, T) [with T = const EmpDist; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/serialization.hpp:128:27: [ skipping 105 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::export_guid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:408:5: note: template boost::shared_ptr::shared_ptr(const boost::weak_ptr&, boost::detail::sp_nothrow_tag)
shared_ptr( weak_ptr const & r, boost::detail::sp_nothrow_tag )
^
../boost/smart_ptr/shared_ptr.hpp:408:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: ‘const boost::shared_ptr’ is not derived from ‘const boost::weak_ptr’
: first(__p.first), second(__p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:399:14: note: template boost::shared_ptr::shared_ptr(const boost::weak_ptr&)
explicit shared_ptr( weak_ptr const & r ): pn( r.pn ) // may throw
^
../boost/smart_ptr/shared_ptr.hpp:399:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: ‘const boost::shared_ptr’ is not derived from ‘const boost::weak_ptr’
: first(__p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:373:41: note: template<class Y, class D, class A> boost::shared_ptr::shared_ptr(Y, D, A)
template<class Y, class D, class A> shared_ptr( Y * p, D d, A a ): px( p ), pn( p, d, a )
^
../boost/smart_ptr/shared_ptr.hpp:373:41: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(__p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:358:32: note: template<class Y, class D> boost::shared_ptr::shared_ptr(Y, D)
template<class Y, class D> shared_ptr( Y * p, D d ): px( p ), pn( p, d )
^
../boost/smart_ptr/shared_ptr.hpp:358:32: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(__p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:347:14: note: template boost::shared_ptr::shared_ptr(Y)
explicit shared_ptr( Y * p ): px( p ), pn() // Y must be complete
^
../boost/smart_ptr/shared_ptr.hpp:347:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(__p.first), second(__p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:334:5: note: boost::shared_ptr::shared_ptr() [with T = void]
shared_ptr() BOOST_NOEXCEPT : px( 0 ), pn() // never throws in 1.30+
^
../boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate expects 0 arguments, 1 provided
../boost/smart_ptr/shared_ptr.hpp:323:25: note: boost::shared_ptr::shared_ptr(const boost::shared_ptr&)
template class shared_ptr
^
../boost/smart_ptr/shared_ptr.hpp:323:25: note: no known conversion for argument 1 from ‘const boost::shared_ptr’ to ‘const boost::shared_ptr&’
In file included from ../boost/system/system_error.hpp:14:0,
from ../boost/thread/exceptions.hpp:22,
from ../boost/thread/pthread/thread_data.hpp:10,
from ../boost/thread/thread_only.hpp:17,
from ../boost/thread/thread.hpp:12,
from ../boost/thread.hpp:13,
from common.h:47,
from hits.h:23,
from abundances.h:23,
from abundances.cpp:16:
../boost/system/error_code.hpp: At global scope:
../boost/system/error_code.hpp:221:36: warning: ‘boost::system::posix_category’ defined but not used [-Wunused-variable]
static const error_category & posix_category = generic_category();
^
../boost/system/error_code.hpp:222:36: warning: ‘boost::system::errno_ecat’ defined but not used [-Wunused-variable]
static const error_category & errno_ecat = generic_category();
^
../boost/system/error_code.hpp:223:36: warning: ‘boost::system::native_ecat’ defined but not used [-Wunused-variable]
static const error_category & native_ecat = system_category();
^
make[2]: *** [abundances.o] Error 1
make[2]: Leaving directory /home/user/Downloads/bioinformatics/cufflinks-master/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/home/user/Downloads/bioinformatics/cufflinks-master'
make: *** [all] Error 2

Web documentation displays all double hyphens as n-dash.
e.g. on http://cole-trapnell-lab.github.io/cufflinks/cuffnorm/index.html:
-o/–output-dir
instead of
-o/--output-dir

To make Cufflinks more compatible with the suite of R/BioC packages for differential expression testing, would it be possible to output un-normalized count data in addition to the other things it does. Is there another way to get this info?

cuffdiff -o diff/ -L input1,input2 -u merged.gtf a.sam b.sam, A eror occured.

 terminate called after throwing an instance of 'std::bad_alloc'
 what():  std::bad_alloc
 Aborted (core dumped)

backtrace info

(gdb) backtrace 
#0  0x00000037332328a5 in raise () from /lib64/libc.so.6
#1  0x0000003733234085 in abort () from /lib64/libc.so.6
#2  0x00007ffff7724a7d in __gnu_cxx::__verbose_terminate_handler() () from     /usr/lib64/libstdc++.so.6
#3  0x00007ffff7722bd6 in ?? () from /usr/lib64/libstdc++.so.6 
#4  0x00007ffff7722c03 in std::terminate() () from /usr/lib64/libstdc++.so.6
#5  0x00007ffff7722d22 in __cxa_throw () from /usr/lib64/libstdc++.so.6
#6  0x00007ffff772311d in operator new(unsigned long) () from /usr/lib64/libstdc++.so.6
#7  0x00007ffff77023c9 in std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_create(unsigned long, unsigned long, std::allocator<char> const&) () from /usr/lib64/libstdc++.so.6
#8  0x00007ffff770319b in std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_M_clone(std::allocator<char> const&, unsigned long) () from /usr/lib64/libstdc++.so.6
#9  0x00007ffff77035ec in std::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long) () from /usr/lib64/libstdc++.so.6
#10 0x00007ffff7703771 in std::basic_string<char, std::char_traits<char>, std::allocator<char> >::append(unsigned long, char) () from /usr/lib64/libstdc++.so.6
#11 0x00007ffff79a9642 in boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits<char> >::load(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&) () from boost/lib/libboost_serialization.so.1.59.0
#12 0x00007ffff79a97da in boost::archive::basic_binary_iarchive<boost::archive::binary_iarchive>::init() () from boost/lib/libboost_serialization.so.1.59.0
#13 0x00000000004322b7 in boost::archive::binary_iarchive_impl<boost::archive::binary_iarchive, char, std::char_traits<char> >::init (this=0x9705e0, flags=0) at boost/include/boost/archive/binary_iarchive_impl.hpp:64
#14 0x000000000042876c in boost::archive::binary_iarchive_impl<boost::archive::binary_iarchive, char, std::char_traits<char> >::binary_iarchive_impl (this=0x9705e0, is=..., flags=0) at boost/include/boost/archive/binary_iarchive_impl.hpp:93
#15 0x000000000041eec7 in boost::archive::binary_iarchive::binary_iarchive (this=0x9705e0, is=..., flags=0) at boost/include/boost/archive/binary_iarchive.hpp:44
#16 0x0000000000421c3b in PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory (this=0x973ba0, 
expression_file_name="a.sam", insert_table=..., reference_table=...) at hits.h:818
#17 0x00000000004174df in driver (ref_gtf=0x9702b0, mask_gtf=0x0, contrast_file=0x0, norm_standards_file=0x0, sam_hit_filename_lists=std::vector of length 2, capacity 2 = {...}, outfiles=...) at cuffdiff.cpp:1580
#18 0x000000000041e259 in main (argc=9, argv=0x7fffffffd068) at cuffdiff.cpp:2684

samtools/samtools#403

the instructions in your getting started page are somewhat old, as is the manner in which libbam is being depended on. Perhaps switching to htslib would make more sense than doing what tophat's group did and freezing samtools versions.

needed to set LIBS=-lrt when running configure to sidestep this problem.

I found that the maximal number of rows in the generated genes.fpkm_tracking from cufflinks -G is somehow capped to 57817, even if there are more gene entries (than 57817) in the input annotation GTF. Now sure if anyone else notice this. I cannot find a similar issue report online.

The cuffflinks I am using is v2.2.1, linked against Boost version 104700.

The GTF file I am using is from GENCODE v19: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz

The command I am using is:
cufflinks -p 4 -G gencode.v19.annotation.gtf input.bam

I want to run multiple cuffmerge tasks under one directory (such as ./), and each task has its unique output subdirectory (indicating using -o option, such as ./cuffmerge/). However, I found cuffmerge created tmp_meta_asm* files under the parent directory (./) instead of the indicated subdirectory (./cuffmerge/). I am wondering whether all the tasks will use the same files and interact with each others. So why does not cuffmerge create tmp_meta_asm* files in cuffmerge output directory?

Hello,

I tried pulling the git to install the latest version, but right off the bat there are problems because the instructions on your site are for installing 0.7.0 from a tarball, not from a git pull.

After pulling the git there are three actual programs I can run:

1. autogen.sh which fails with the error:
   ./autogen.sh: 19: ./autogen.sh: ./version.sh: not found

   
fatal: Not a git repository (or any parent up to mount point /genome)

   
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

   
./autogen.sh: 21: ./autogen.sh: autoreconf: not found

2. configure.ac which fails with the error:
   ./configure.ac: line 1: syntax error near unexpected token `[ax_boost_base.m4]'

./configure.ac: line 1: `m4_include([ax_boost_base.m4])'

3. make_bin.sh which only gives the unexplained output:
   Usage:

   
./make_bin.sh <package_base_name> <boost_prefix> [<bam_prefix> [<Eigen_prefix>]]

I have boost, samtools, and eigen all in PATH exported directories or default shared directories (ie /usr/local/include/) but it didn't pickup that they are readily readable. Manually entering the locations, completely guessing on what package_base_name is, and trying ./make_bin.sh again fails with the error:
packing up cufflinks_git.tar.gz, using boost in /usr/lib/x86_64-linux-gnu/, linking against /usr/local/include/bam/ and using BAM in /usr/local/include/Eigen/, using Eigen in
make: *** No rule to make target distclean'. Stop.<p> ./make_bin.sh: line 17: [: missing]'


Unrecognized architecture


./make_bin.sh: line 42: ./configure: No such file or directory


make: *** No targets specified and no makefile found. Stop.


cp: cannot stat ‘src/cufflinks’: No such file or directory


cp: cannot stat ‘src/cuffcompare’: No such file or directory


cp: cannot stat ‘src/cuffdiff’: No such file or directory


cp: cannot stat ‘src/gffread’: No such file or directory


cp: cannot stat ‘src/gtf_to_sam’: No such file or directory


cp: cannot stat ‘src/cuffnorm’: No such file or directory


cp: cannot stat ‘src/cuffquant’: No such file or directory


cufflinks_git/


cufflinks_git/README


cufflinks_git/AUTHORS


cufflinks_git/LICENSE


cufflinks_git/cuffmerge

Which says that my command, which follows the provided usage instructions that lack any supporting explanation, is missing at least one parameter identifying linking against. It also is looking for 8 files that aren't even in the git pull configure (I tried editing to point at configure.ac but this still failed with the same message as above,src/cufflinks, src/cuffcompare, src/cuffdiff, src/gffread, scr/gff_to_sam, src/cuffnorm, and src/cuffquant which appear to be all of the cufflinks suite programs.

With no idea what is trying to be done and no way to move forward I'm stuck here unless I get the precompiled binaries mentioned on the cufflinks website making this git useless for acquiring a version of cufflinks.

With ~130 samples, and cxb files of about 20GB in sum, cuffnorm 2.2.1 seems to use more than 80GB of memory. Is that expected, and can I do anything to reduce the memory consumption?

There seems to be an acknowledged incompatibility of the most recent cufflinks 2.2.1 that makes it incompatible to certain (standard-compliant) SAM inputs. Specifically, one has to expect the critical Error (GFaSeqGet): subsequence cannot be larger than 16569 from cufflinks if bias modeling is turned on (as it should). This error results from the inability of cufflinks to model softclipped bases that extend over the end of the chromosome (a circumstance that is not forbidden by the SAM specs).

Since the RNA-Seq aligner STAR sometimes generates such outputs if a read best fits to the chromosomal end (this can happen in general and specifically in cancer genomes due to chromosomal rearrangements), there are two ways to post-process STAR BAMs to cut off the ends and make cufflinks eat the input file. Still, I would like to avoid generating yet another copy of a BAM file just for cufflinks since other quantitation methods deal with softclipped bases just fine and the error seems to be with cufflinks, so that's why I'd appreciate a fix from your end. The linked mail thread contains additional information and SAM examples. Thank you.

This issue is co-tracked in bcbio.

Please see if you can reproduce the following issue:
When I ran the following command, I get the output shown below (bam file available at https://dl.dropboxusercontent.com/u/34969406/test.bam)

cufflinks -p 4 -o test_out test.bam
You are using Cufflinks v2.2.2, which is the most recent release.
[16:48:01] Inspecting reads and determining fragment length distribution.

Processed 1 loci. [_] 100%
Map Properties:
Normalized Map Mass: 151067.00
Raw Map Mass: 151067.00
Fragment Length Distribution: Empirical (learned)
Estimated Mean: 241.42
Estimated Std Dev: 72.75
[16:48:02] Assembling transcripts and estimating abundances.
Processed 0 loci. [_] 100%

When I ran the command using v2.2.1, either pre-built, or a version I built from source from here:https://github.com/smowton/cufflinks, I get the following output:

[16:48:38] Inspecting reads and determining fragment length distribution.

Processed 2 loci. [_] 100%
Map Properties:
Normalized Map Mass: 151371.54
Raw Map Mass: 151371.54
Fragment Length Distribution: Empirical (learned)
Estimated Mean: 241.41
Estimated Std Dev: 72.75
[16:48:39] Assembling transcripts and estimating abundances.
Processed 2 loci. [_] 100%

Is this simply due to differences in the default options, or is there a bug in v2.2.2? Thanks for your help and advice!

The locfit component is distributed without the README file. The licence it contains says it must be included.
Unfortunately it contains a usage restriction which is considered to make it non-free (e.g. by Debian and potential Fedora packagers) and brings the cufflinks distribution under licence terms which are not simply Boost's:

Locfit code, as distributed, should not, and can not, be used to derive meaningful benchmarks, either or the speed or accuracy of algorithms. Anyone wishing to use Locfit in any kind of comparative benchmark study must contact and obtain permission from the Author.

The R package for it on CRAN contains a version with a free licence, but it isn't a drop-in replacement for the bundled one.

Empty lines between fasta entries in file provided via the -g switch throws error at line 117 in GFastaIndex.cpp

Workaround is either to pre-index file with samtools - handles blank lines fine - or remove blank line in fasta file.

Hi,

The problem is that in RSQLite the function sqliteQuickSQL has been deprecated, so it cannot be used anymore, and programs that used to work now don't work with an updated R.

So cufflink cannot be installed with the last R version, it says:

Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
Error: package ‘Gviz’ could not be loaded

Could someone solve that problem ?

Thanks,

Rafael

It is extremely helpful for folks trying to grab/correlate specific versions to be able to:

git clone repo/address.git
git checkout vX.X.X

It also helps greatly when building package recipes for things like conda which is what I am doing now.

Thanks

When I run cuffnorm (v2.2.1 (4237)) on single CXB file, I received a error massage "Error: cuffdiff requires at least 2 SAM files".

I found the corresponding code in cuffnorm.cpp.
cuffnorm.cpp

Can't I apply cuffnorm on single CXB file?

I have SAM files that are different from general SAM files. For a given FASTQ data from RNA-Seq project, we first collapsed the reads in terms of sequence content to get rid of redundancy and obtain a much smaller FASTA file, like

1_356780
ATGACTA....
2_234565
AAATTTTCAT...

Here, the expression information or count is embedded inside the sequence name. For the above example, the first sequence has 356780 copies or count within the individual FASTQ data, while the second sequence has 234565 copies. Such collapsing really saved us a lot of time in read-to-genome mapping. Consequently, in our SAM file obtained using this collapsed reads, the expression count data for each collapsed read is also embedded inside the name.

My question is how can we use cuffquant for our special SAM files generated using collapsed reads? Can we use this kind of SAM file to get expression data for individual genes/transcripts from cufflinks, and then multiple the expression data with the aforementioned expression counts to get the final expression count number? I am afraid that this multiplication might not be correct and will inflate the expression number. Any comment or suggestion will be highly appreciated.

Hi,
with the latest commit (commit 815e435) I get the following error while running make (after configure):
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -DNDEBUG -pthread -I/usr/include -I/usr/include -MT clustering.o -MD -MP -MF .deps/clustering.Tpo -c -o clustering.o clustering.cpp In file included from clustering.h:38:0, from clustering.cpp:10: abundances.h:21:23: fatal error: Eigen/Dense: No such file or directory #include <Eigen/Dense> ^ compilation terminated.

The path is /usr/include/eigen3/Eigen/Dense on my system (Archlinux, nothing special here). I have seen your code tries to check for its presence with ax_check_eigen.m4, but it fails.
I see this line: AS_HELP_STRING([--with-eigen@<:@=DIR@:>@], [use EIGEN libraries (default is yes) - it is possible to specify the root directory for EIGEN (optional)]): could you precise how to do so?
I tried running make with -I/usr/include/eigen3, to no avail. The makefile has a line in EIGEN_CPPFLAGS = (no value).
Thanks a lot for your help!

In the getting started section:
http://cole-trapnell-lab.github.io/cufflinks/getting_started/

http://cufflinks.cbcb.umd.edu/downloads/test_data.sam

Should the link point to?

https://raw.githubusercontent.com/cole-trapnell-lab/cufflinks/master/doc/html/downloads/test_data.sam

In your Nature Biotechnology paper, 2013 31(1):46-53, you have described Cuffdiff 2.

I already obtained SAM files after aligning RNA-Seq reads to the reference genome. I only need to use Cuffdiff 2 to conduct the downstream analysis. Where can I download the codes for Cuffdiff 2, as described in this paper? Thank you for clarification.

I took a 150kb region from H. saltator and simulated Illumina reads from the transcripts encoded in that region. The idea was to use the data for instruction: teach the students basic RNA-seq analysis with Bowtie/Tophat/Cufflinks. See the data set on figshare.

All of the data files are included in the tar.gz file, and the run.sh file shows the processing procedure. If I run the shell script as-is, it fails non-deterministically on one of the Cufflinks commands (never the same one). I can fix this by taking out the --frag-len-mean and --frag-len-std-dev options, which I put in when the program complained that it was having a hard time estimating these from limited data. So without these options, Tophat, Cufflinks, and Cuffmerge will execute successfully, but then Cuffdiff will segfault. Any idea what the issue might be?

I'm using Bowtie2 2.2.4, Tophat 2.0.13, and Cufflinks 2.2.1 on Mac OS 10.10.2.

There seem to be many places where boost random number generators are instantiated (e.g. boost::mt19937 rng; in simulate_count_covariance) but without a specified seed. So the default seed for the generator is used. Seems like they should be seeded with some function of the user-defined --seed value. I noticed this because I see some isoforms for which the coverage estimate varies a lot when the BAM is perturbed slightly, but which do not vary when --seed is varied.

Ben

The develop branch of cuffquant.cpp lists "-c/--min-alignment-count" as an option in the usage (line 107), but there is no code to handle this option

Hello All,
Cufflinks is not recognizing the option --library-norm-method while finding the transcript abundance.
while using it on the following command line

cufflinks --num-threads 10 --quiet --no-update-check --max-bundle-frags 2000000 --library-type fr-unstranded --frag-bias-correct --library-norm-method /human_genome37.fa --multi-read-correct --GTF-guide /ref-transcripts.gtf --output-dir BM_CR_pat_4.txt BM_CR_pat_4.bam
and its throwing following error,

Error: file/directory --library-norm-method does not exist!

Here's the gff3 file: ftp://ftp.ensemblgenomes.org/pub/release-24/plants/gff3/oryza_sativa/Oryza_sativa.IRGSP-1.0.24.gff3

tophat accepted this file without obvious errors.

Here's the backtrace (just downloaded 2.2.1)

Program received signal SIGSEGV, Segmentation fault.
0x000000378a680b51 in __strlen_sse2 () from /lib64/libc.so.6
(gdb) bt
#0  0x000000378a680b51 in __strlen_sse2 () from /lib64/libc.so.6
#1  0x0000000000542cfd in GffObj::parseAttrs (this=0x8b7b00, atrlist=@0x8b7bf0, info=0x0, isExon=false) at gff.cpp:1379
#2  0x0000000000544155 in GffObj::addExon (this=0x8b7b00, reader=<value optimized out>, gl=0x8b3c40, keepAttr=true, noExonAttr=true) at gff.cpp:522
#3  0x00000000005452d0 in GffObj::GffObj (this=0x8b7b00, gfrd=0x7fffffffc020, gffline=0x8b3c40, keepAttr=true, noExonAttr=true) at gff.cpp:827
#4  0x0000000000545aa2 in GffReader::newGffRec (this=0x7fffffffc020, gffline=0x8b3c40, keepAttr=<value optimized out>, noExonAttr=true, parent=0x0,
    pexon=0x0, glst=0x0) at gff.cpp:999
#5  0x00000000005464dc in GffReader::readAll (this=0x7fffffffc020, keepAttr=true, mergeCloseExons=true, noExonAttr=true) at gff.cpp:1228
#6  0x000000000054fb22 in read_transcripts (f=0x88d320, seqdata=..., crc_result=..., keepAttrs=true) at gtf_tracking.cpp:600
#7  0x00000000004a8c4a in load_ref_rnas (ref_mRNA_file=0x88d320, rt=..., ref_mRNAs=..., gtf_crc_result=..., loadSeqs=false, loadFPKM=false)
    at bundles.cpp:104
#8  0x000000000040f014 in driver (hit_file_name=<value optimized out>, ref_gtf=0x88d320, mask_gtf=0x0) at cufflinks.cpp:1623
#9  0x000000000042477a in main (argc=14, argv=<value optimized out>) at cufflinks.cpp:1799