PASA memory issue with sample data
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Jacky Hess
Apr 28, 2015, 10:59:18 AM4/28/15
to pasapipel...@googlegroups.com
Hi there,
I am trying to get PASA running with the sample data set and I'm running into a memory allocation issue which I can't figure out how to fix.
This is the command line I'm executing:
perl ../scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS blat,gmap --CPU 1
The pipeline gets up to the "/Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/..//scripts/assemble_clusters.dbi " command without problems, but then starts gulping up memory and crashes with segmentation fault:
....
## Processing CMD: 22/33
16:37:29 CMD: /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/..//scripts/reassign_clusters_via_valid_align_coords.dbi -M sample_mydb_pasa > pasa_run.log.dir/cluster_reassignment_by_valid_alignment_coords.default.out
-reassigning clusters on scaffold: gi|rev68722 Thread(27) SUCCESS CMD: unknown Time to complete: 0 seconds
Thread(28) SUCCESS CMD: unknown Time to complete: 0 seconds
Thread(29) SUCCESS CMD: unknown Time to complete: 0 seconds
Thread(30) SUCCESS CMD: unknown Time to complete: 0 seconds
[30/30] - loading cluster reassignments for scaffold: gi|rev68725
Done.
## Processing CMD: 23/33
16:37:38 CMD: /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/..//scripts/assemble_clusters.dbi -G genome_sample.fasta -M sample_mydb_pasa -T 1 > sample_mydb_pasa.pasa_alignment_assembly_building.ascii_illustrations.out
sh: line 1: 46022 Segmentation fault: 11 /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/../bin/pasa /var/folders/bp/57q11_p55353yzfmt54lsbf000705d/T//pasa.1430231858-0.504954500430362.+.in > /var/folders/bp/57q11_p55353yzfmt54lsbf000705d/T//pasa.1430231858-0.504954500430362.+.out
PASA died on input file. See pasa_killer.inputThread 1 terminated abnormally: Died at /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/..//PerlLib//CDNA/PASA_alignment_assembler.pm line 262.
ERROR, thread 1 exited with error Died at /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/..//PerlLib//CDNA/PASA_alignment_assembler.pm line 262.
sh: line 1: 46068 Segmentation fault: 11 /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/../bin/pasa /var/folders/bp/57q11_p55353yzfmt54lsbf000705d/T//pasa.1430231859-0.410819630445079.+.in > /var/folders/bp/57q11_p55353yzfmt54lsbf000705d/T//pasa.1430231859-0.410819630445079.+.out
At which point I have to kill the process because it is consuming most of my memory. See attached for the full log.
I'm running on a Macbook Pro, 16GB RAM with OSX 10.9.5 (Mavericks).
Thanks very much for your help!
Best,
Jacky
Jacky Hess
May 7, 2015, 8:18:53 AM5/7/15
to pasapipel...@googlegroups.com
Hello again,
I am still grappling with this issue. I wonder if someone could comment on what the typical memory usage is for PASA. Is 16 GB simply not enough? I am trying to work with a 40 MB fungal genome.
Best,
Jacky
Jaqueline Hess
May 7, 2015, 11:11:26 AM5/7/15
to pasapipel...@googlegroups.com
One last email about this. I think I was able to isolate the problem:
The problem lies with the pasa executable itself. I’ve recompiled:
cd pasa_cpp
make clean
make
Trying to run the sample data in the pasa_cpp directory throws the same bad_alloc error that I see in the pipeline output:
./pasa pasa_cpp_sample_input3
….
pasa(35032,0x7fff7469b310) malloc: *** mach_vm_map(size=10520408740576890880) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
libc++abi.dylib: terminating with uncaught exception of type std::bad_alloc: std::bad_alloc
Abort trap: 6
This seems to be a Mac-specific problem. Installing PASA on a linux machine on the cluster and running the same command works fine.
Sadly I can’t run MySQL on our cluster, but I will try to find a linux machine elsewhere which should hopefully solve this problem.
Best,
Jacky
On 07 May 2015, at 14:18, Jacky Hess <jaqueli...@gmail.com> wrote:
Hello again,I am still grappling with this issue. I wonder if someone could comment on what the typical memory usage is for PASA. Is 16 GB simply not enough? I am trying to work with a 40 MB fungal genome.Best,
Jacky
On Tuesday, April 28, 2015 at 4:59:18 PM UTC+2, Jacky Hess wrote:
Hi there,I am trying to get PASA running with the sample data set and I'm running into a memory allocation issue which I can't figure out how to fix.This is the command line I'm executing:
perl ../scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS blat,gmap --CPU 1
The pipeline gets up to the "/Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/..//scripts/assemble_clusters.dbi " command without problems, but then starts gulping up memory and crashes with segmentation fault:
....
## Processing CMD: 22/33
16:37:29 CMD: /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/..//scripts/reassign_clusters_via_valid_align_coords.dbi -M sample_mydb_pasa > pasa_run.log.dir/cluster_reassignment_by_valid_alignment_coords.default.out
-reassigning clusters on scaffold: gi|rev68722 Thread(27)SUCCESS CMD: unknown Time to complete: 0 seconds
Thread(28) SUCCESS CMD: unknown Time to complete: 0 seconds
Thread(29) SUCCESS CMD: unknown Time to complete: 0 seconds
Thread(30) SUCCESS CMD: unknown Time to complete: 0 seconds
[30/30] - loading cluster reassignments for scaffold: gi|rev68725
Done.
## Processing CMD: 23/33
16:37:38 CMD: /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/..//scripts/assemble_clusters.dbi -G genome_sample.fasta -M sample_mydb_pasa -T 1 > sample_mydb_pasa.pasa_alignment_assembly_building.ascii_illustrations.out
sh: line 1: 46022 Segmentation fault: 11 /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/../bin/pasa /var/folders/bp/57q11_p55353yzfmt54lsbf000705d/T//pasa.1430231858-0.504954500430362.+.in > /var/folders/bp/57q11_p55353yzfmt54lsbf000705d/T//pasa.1430231858-0.504954500430362.+.out
PASA died on input file. See pasa_killer.inputThread 1 terminated abnormally: Died at /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/..//PerlLib//CDNA/PASA_alignment_assembler.pm line 262.
ERROR, thread 1 exited with error Died at /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/..//PerlLib//CDNA/PASA_alignment_assembler.pm line 262.
sh: line 1: 46068 Segmentation fault: 11 /Users/jacqueh/Research/Software/PASApipeline-2.0.1/scripts/../bin/pasa /var/folders/bp/57q11_p55353yzfmt54lsbf000705d/T//pasa.1430231859-0.410819630445079.+.in > /var/folders/bp/57q11_p55353yzfmt54lsbf000705d/T//pasa.1430231859-0.410819630445079.+.out
At which point I have to kill the process because it is consuming most of my memory. See attached for the full log.
I'm running on a Macbook Pro, 16GB RAM with OSX 10.9.5 (Mavericks).
Thanks very much for your help!
Best,
Jacky
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Will Holtz
May 7, 2015, 12:09:02 PM5/7/15
to Jaqueline Hess, pasapipel...@googlegroups.com
You could install VirtualBox and run a linux virtual machine on your mac.
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Brian Haas
May 8, 2015, 4:04:30 AM5/8/15
to Will Holtz, Jaqueline Hess, pasapipeline-users
Hi Jaqueline,
Could you send me the file:
/var/folders/bp/57q11_p55353yzfmt54lsbf000705d/T//pasa.1430231858-0.504954500430362.+.in
which pasa is crashing on? I'm hoping it'll offer some clues.
sorry for the delayed response... I've been traveling.
best,
~brian
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Jaqueline Hess
May 13, 2015, 7:32:35 AM5/13/15
to Brian Haas, Will Holtz, pasapipeline-users
Hi Brian,
No worries! I’ve managed to get an instance running just fine now using VirtualBox Ubuntu (Thanks Will!).
I don’t think I have the input from the command below. It looks like it cleans itself up before I can get to it. I’m attaching pass_killer.input instead.
Brian Haas
May 13, 2015, 7:43:48 PM5/13/15
to Jaqueline Hess, Will Holtz, pasapipeline-users
Thanks, Jacky.
I tried running the pasa assembler on that file and it seemed to work just fine, so maybe there was just a glitch of some sort earlier.
wme18-ed2:Downloads bhaas$ pasa pasa_killer.input
//
input: blat.proc22290.chain_6797,+,8897-9207,9290-9396,9477-9560,9655-9730,10021-10065,10165-10209
input: blat.proc22293.chain_6797,+,8897-9207,9290-9396,9477-9560,9655-9730,10021-10065,10165-10209
input: gi|19875340|gb|AU236171.1|AU236171.path1,+,8938-9207,9290-9392
input: c863_g0_i1.path1,+,8938-9207,9290-9392
input: blat.proc22290.chain_6821,+,8939-9207,9290-9396,9477-9487
input: blat.proc22293.chain_6821,+,8939-9207,9290-9396,9477-9487
input: blat.proc22290.chain_12424,+,8958-9207,9290-9396,9477-9560,9655-9680
input: gi|86066808|gb|DR362565.1|DR362565.path1,+,8958-9207,9290-9393
input: c6584_g0_i1.path1,+,8958-9207,9290-9393
input: align_26167,+,8958-9207,9290-9396,9477-9560,9655-9680
input: blat.proc22293.chain_7752,+,8959-9207,9290-9396,9477-9508
input: gi|59846715|gb|BP810636.1|BP810636.path1,+,8959-9207,9290-9396,9477-9511
input: c3710_g0_i1.path1,+,8959-9207,9290-9396,9477-9511
input: align_7683,+,8959-9207,9290-9396,9477-9508
input: gi|42469342|emb|BX818792.1|CNS0A9WU.path1,+,8978-9207,9290-9396,9477-9560,9655-9730,10021-10065,10165-10539,10620-10688,10800-10864,10953-11021,11096-11168,11249-11353,11471-11542,11627-11689,11778-12068
input: c1877_g0_i1.path1,+,8978-9207,9290-9396,9477-9560,9655-9730,10021-10065,10165-10539,10620-10688,10800-10864,10953-11021,11096-11168,11249-11353,11471-11542,11627-11689,11778-12068
input: gi|42455259|emb|BX842025.1|CNS09Y86.path1,+,8985-9207,9290-9396,9477-9560,9655-9730,10021-10065,10165-10539,10620-10688,10800-10864,10953-11021,11096-11168,11249-11353,11471-11542,11627-11689,11778-12181
input: c1679_g0_i1.path1,+,8985-9207,9290-9396,9477-9560,9655-9730,10021-10065,10165-10539,10620-10688,10800-10864,10953-11021,11096-11168,11249-11353,11471-11542,11627-11689,11778-12181
input: align_3760,+,9013-9207,9290-9396,9477-9560,9655-9730,10021-10065,10165-10438
input: align_17579,+,9013-9207,9290-9396,9477-9560,9655-9730,10021-10065,10165-10438
input: align_6048,+,9023-9207,9290-9396,9477-9560,9655-9730,10021-10065,10165-10539,10620-10688,10800-10864,10953-11021,11096-11168,11249-11353,11471-11542,11627-11689,11778-12171
input: align_19867,+,9023-9207,9290-9396,9477-9560,9655-9730,10021-10065,10165-10539,10620-10688,10800-10864,10953-11021,11096-11168,11249-11353,11471-11542,11627-11689,11778-12171
input: gi|86087708|gb|DR383467.1|DR383467.path2,+,11273-11353,11471-11542,11627-11689,11778-12192
input: c6775_g0_i1.path2,+,11273-11353,11471-11542,11627-11689,11778-12192
input: gi|49317832|gb|BP666329.1|BP666329.path1,+,11503-11542,11627-11689,11778-12106
input: c3065_g0_i1.path1,+,11503-11542,11627-11689,11778-12106
input: gi|19741647|gb|AU227000.1|AU227000.path1,+,11519-11542,11627-11689,11778-12075
input: gi|49031483|gb|BP582273.1|BP582273.path1,+,11519-11542,11627-11689,11778-12075
input: c287_g0_i1.path1,+,11519-11542,11627-11689,11778-12075
input: c2348_g0_i1.path1,+,11519-11542,11627-11689,11778-12075
input: blat.proc22290.chain_4281,+,11532-11542,11627-11689,11778-12075
input: blat.proc22293.chain_4281,+,11532-11542,11627-11689,11778-12075
input: blat.proc22290.chain_4257,+,11535-11542,11627-11689,11778-12075
input: align_18032,+,11535-11542,11627-11689,11778-12075
input: blat.proc22290.chain_4781,+,11789-12222
input: blat.proc22293.chain_4781,+,11789-12222
input: align_4807,+,11796-12222
input: align_18626,+,11796-12222
Individual Alignments: (38)
-------><--><-> <-> <> <- (+) blat.proc22290.chain_6797 index: [0]
-------><--><-> <-> <> <- (+) blat.proc22293.chain_6797 index: [1]
------><-- (+) gi|19875340|gb|AU236171.1|AU236171.path1 index: [2]
------><-- (+) c863_g0_i1.path1 index: [3]
------><-->< (+) blat.proc22290.chain_6821 index: [4]
------><-->< (+) blat.proc22293.chain_6821 index: [5]
------><--><-> < (+) align_26167 index: [6]
------><-- (+) c6584_g0_i1.path1 index: [7]
------><-- (+) gi|86066808|gb|DR362565.1|DR362565.path1 index: [8]
------><--><-> < (+) blat.proc22290.chain_12424 index: [9]
------><--><- (+) blat.proc22293.chain_7752 index: [10]
------><--><- (+) gi|59846715|gb|BP810636.1|BP810636.path1 index: [11]
------><--><- (+) c3710_g0_i1.path1 index: [12]
------><--><- (+) align_7683 index: [13]
-----><--><-> <-> <> <-------><-> <> <-><-> <-> <-><-> <------ (+) gi|42469342|emb|BX818792.1|CNS0A9WU.path1 index: [14]
-----><--><-> <-> <> <-------><-> <> <-><-> <-> <-><-> <------ (+) c1877_g0_i1.path1 index: [15]
-----><--><-> <-> <> <-------><-> <> <-><-> <-> <-><-> <-------- (+) gi|42455259|emb|BX842025.1|CNS09Y86.path1 index: [16]
-----><--><-> <-> <> <-------><-> <> <-><-> <-> <-><-> <-------- (+) c1679_g0_i1.path1 index: [17]
-----><--><-> <-> <> <----- (+) align_17579 index: [18]
-----><--><-> <-> <> <----- (+) align_3760 index: [19]
----><--><-> <-> <> <-------><-> <> <-><-> <-> <-><-> <-------- (+) align_6048 index: [20]
----><--><-> <-> <> <-------><-> <> <-><-> <-> <-><-> <-------- (+) align_19867 index: [21]
--> <-><-> <-------- (+) gi|86087708|gb|DR383467.1|DR383467.path2 index: [22]
--> <-><-> <-------- (+) c6775_g0_i1.path2 index: [23]
-><-> <------- (+) gi|49317832|gb|BP666329.1|BP666329.path1 index: [24]
-><-> <------- (+) c3065_g0_i1.path1 index: [25]
-><-> <------ (+) c2348_g0_i1.path1 index: [26]
-><-> <------ (+) c287_g0_i1.path1 index: [27]
-><-> <------ (+) gi|49031483|gb|BP582273.1|BP582273.path1 index: [28]
-><-> <------ (+) gi|19741647|gb|AU227000.1|AU227000.path1 index: [29]
-><-> <------ (+) blat.proc22290.chain_4281 index: [30]
-><-> <------ (+) blat.proc22293.chain_4281 index: [31]
><-> <------ (+) blat.proc22290.chain_4257 index: [32]
><-> <------ (+) align_18032 index: [33]
---------- (+) blat.proc22290.chain_4781 index: [34]
---------- (+) blat.proc22293.chain_4781 index: [35]
---------- (+) align_4807 index: [36]
---------- (+) align_18626 index: [37]
ASSEMBLIES: (1)
-------><--><-> <-> <> <-------><-> <> <-><-> <-> <-><-> <--------- (+) assembly_0 score: (38) contains [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37]
assembly: (0) contains alignments: [blat.proc22290.chain_6797,blat.proc22293.chain_6797,gi|19875340|gb|AU236171.1|AU236171.path1,c863_g0_i1.path1,blat.proc22290.chain_6821,blat.proc22293.chain_6821,align_26167,c6584_g0_i1.path1,gi|86066808|gb|DR362565.1|DR362565.path1,blat.proc22290.chain_12424,blat.proc22293.chain_7752,gi|59846715|gb|BP810636.1|BP810636.path1,c3710_g0_i1.path1,align_7683,gi|42469342|emb|BX818792.1|CNS0A9WU.path1,c1877_g0_i1.path1,gi|42455259|emb|BX842025.1|CNS09Y86.path1,c1679_g0_i1.path1,align_17579,align_3760,align_6048,align_19867,gi|86087708|gb|DR383467.1|DR383467.path2,c6775_g0_i1.path2,gi|49317832|gb|BP666329.1|BP666329.path1,c3065_g0_i1.path1,c2348_g0_i1.path1,c287_g0_i1.path1,gi|49031483|gb|BP582273.1|BP582273.path1,gi|19741647|gb|AU227000.1|AU227000.path1,blat.proc22290.chain_4281,blat.proc22293.chain_4281,blat.proc22290.chain_4257,align_18032,blat.proc22290.chain_4781,blat.proc22293.chain_4781,align_4807,align_18626] with structure [assembly_0,+,8897-9207,9290-9396,9477-9560,9655-9730,10021-10065,10165-10539,10620-10688,10800-10864,10953-11021,11096-11168,11249-11353,11471-11542,11627-11689,11778-12222] score: (38)
I hope this is useful. Thanks very much for your help!
Chirag Parsania
Feb 16, 2016, 2:49:46 AM2/16/16
to pasapipeline-users, jaqueli...@gmail.com, who...@lygos.com
Hi Brian,
I have gone through this post as I am facing same problem. But not able solve by myself. I am running pasa on sample data. Following steps as given on the tutorial page. I am running pasa pipeline using run_sample_pipeline.pl script. I am using just one aligner blat. Following is the error reported by pasa.
pasa(57081,0x7fff7688e000) malloc: *** mach_vm_map(size=18395274366738313216) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
libc++abi.dylib: terminating with uncaught exception of type std::bad_alloc: std::bad_alloc
sh: line 1: 57081 Abort trap: 6 /usr/local/bin/PASA/scripts/../bin/pasa /var/folders/cd/psplt0nn2j5918wr6sv4r1x80000gn/T//pasa.1455608307-0.542612522914173.+.in > /var/folders/cd/psplt0nn2j5918wr6sv4r1x80000gn/T//pasa.1455608307-0.542612522914173.+.out
PASA died on input file. See pasa_killer.inputThread 5 terminated abnormally: Died at /usr/local/bin/PASA/scripts/..//PerlLib/CDNA/PASA_alignment_assembler.pm line 262.
ERROR, thread 5 exited with error Died at /usr/local/bin/PASA/scripts/..//PerlLib/CDNA/PASA_alignment_assembler.pm line 262.
Many many thanks
Chirag
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Brian Haas
Feb 16, 2016, 8:39:01 AM2/16/16
to Chirag Parsania, pasapipeline-users, Jacky Hess, William Holtz
Hi Chirag,
This looks like an out-of-memory issue. Could you send me the file:
/var/folders/cd/psplt0nn2j5918wr6sv4r1x80000gn/T//pasa.1455608307-0.542612522914173.+.in
that's causing the trouble?
many thanks,
~brian
This looks like an out-of-memory issue. Could you send me the file:
/var/folders/cd/psplt0nn2j5918wr6sv4r1x80000gn/T//pasa.1455608307-0.542612522914173.+.in
that's causing the trouble?
many thanks,
~brian
Chirag Parsania
Feb 16, 2016, 9:07:49 AM2/16/16
to pasapipeline-users, chirag....@gmail.com, jaqueli...@gmail.com, who...@lygos.com
HI Brian,
The file you have asked "pasa.1455608307-0.542612522914173.+.in" is not there in my directory. But I have "pasa.1455608307-0.542612522914173.+.out" file. Please find attached.
Brian Haas
Feb 16, 2016, 9:19:25 AM2/16/16
to Chirag Parsania, pasapipeline-users, Jacky Hess, William Holtz
Do you see a file named 'pasa_killer' ? It may have renamed the .in file after it crashed.
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Brian Haas
Feb 16, 2016, 9:29:01 AM2/16/16
to Chirag Parsania, pasapipeline-users, Jacky Hess, William Holtz
Thanks!
OK - you can try to run pasa directly on that file:
pasa pasa_killer.input
It should finish in a fraction of a second and use very little RAM.
This suggests that it is an issue with your server. You might even just try installing a new version of GCC and recompiling everything. On a mac, this is easy to do using homebrew.
best,
~brian
On Tue, Feb 16, 2016 at 9:21 AM, Chirag Parsania <chirag....@gmail.com> wrote:
HI,Yes.. Please find attached.
CheersChirag
Chirag Parsania
Feb 16, 2016, 10:25:54 PM2/16/16
to pasapipeline-users, chirag....@gmail.com, jaqueli...@gmail.com, who...@lygos.com
Hi Brian,
I have updated GCC on my mac. Current version 4.8 and now I am trying to compile PASA once again. But after doing make command I encountered following error. Please help
clang: error: '-I-' not supported, please use -iquote instead
Cheers
Chirag
CheersChirag
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Chirag Parsania
Feb 17, 2016, 4:55:40 AM2/17/16
to pasapipeline-users, chirag....@gmail.com, jaqueli...@gmail.com, who...@lygos.com
Solved from your previous reply
changing line:SEARCHDIRS := -I- -I${ZDIR} -I${THISCODEDIR} -I${TGICLASSDIR}
to
SEARCHDIRS := -I -I${ZDIR} -I${THISCODEDIR} -I${TGICLASSDIR}
Thanks
Chirag
Guna
Apr 18, 2017, 3:46:11 PM4/18/17
to pasapipeline-users, chirag....@gmail.com, jaqueli...@gmail.com, who...@lygos.com
Hi Brian,
I have a similar memory issue when running the pasa annotation step.
I'm trying to annotate a relatively large genome ~2.5G - the pasa transcript alignment step worked fine (thought this might've been a problem for larger genomes from other threads & using gmapl instead could be a solution but no issues here). However, the process dies in the second iteration of running the pasa annotation (first iteration took ~ 1.5 days but it worked).
This is being run on linux server. I have tried running pasa on the pasa_killer.input file and can recreate the issue below.
$ pasa pasa_killer.input
//
input: evm.model.Chr02_genome_PacBio.4107,-,176085462-176086585,176087942-176088997,176088065-176088447
input: asmbl_43989,-,176085462-176086585,176088065-176088447
*** glibc detected *** /ngsprod/gsap/tools/PASA_Dev/bin/pasa: malloc(): memory corruption (fast): 0x0000000000d337e0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x75f3e)[0x7fce6e709f3e]
/lib64/libc.so.6(+0x7a608)[0x7fce6e70e608]
/lib64/libc.so.6(__libc_malloc+0x5c)[0x7fce6e70ebfc]
/mnt/common/rh6/ngsdev/lib64/libstdc++.so.6(_Znwm+0x18)[0x7fce6ef207e8]
/mnt/common/rh6/ngsdev/lib64/libstdc++.so.6(_ZNSs4_Rep9_S_createEmmRKSaIcE+0x59)[0x7fce6ef85ef9]
/mnt/common/rh6/ngsdev/lib64/libstdc++.so.6(_ZNSs4_Rep8_M_cloneERKSaIcEm+0x1b)[0x7fce6ef86b6b]
/mnt/common/rh6/ngsdev/lib64/libstdc++.so.6(_ZNSs7reserveEm+0x30)[0x7fce6ef86c10]
/mnt/common/rh6/ngsdev/lib64/libstdc++.so.6(_ZNSs6appendERKSs+0x38)[0x7fce6ef86ce8]
/ngsprod/gsap/tools/PASA_Dev/bin/pasa[0x403169]
/ngsprod/gsap/tools/PASA_Dev/bin/pasa[0x40afda]
/ngsprod/gsap/tools/PASA_Dev/bin/pasa[0x414f4a]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x7fce6e6b2d1d]
/ngsprod/gsap/tools/PASA_Dev/bin/pasa[0x402439]
======= Memory map: ========
00400000-0041d000 r-xp 00000000 00:28 4440843629 /ngsprod/gsap/tools/PASA_Dev/bin/pasa
0061c000-0061d000 rw-p 0001c000 00:28 4440843629 /ngsprod/gsap/tools/PASA_Dev/bin/pasa
00d31000-00d52000 rw-p 00000000 00:00 0 [heap]
7fce68000000-7fce68021000 rw-p 00000000 00:00 0
7fce68021000-7fce6c000000 ---p 00000000 00:00 0
7fce6e694000-7fce6e81e000 r-xp 00000000 fd:00 4108 /lib64/libc-2.12.so
7fce6e81e000-7fce6ea1e000 ---p 0018a000 fd:00 4108 /lib64/libc-2.12.so
7fce6ea1e000-7fce6ea22000 r--p 0018a000 fd:00 4108 /lib64/libc-2.12.so
7fce6ea22000-7fce6ea24000 rw-p 0018e000 fd:00 4108 /lib64/libc-2.12.so
7fce6ea24000-7fce6ea28000 rw-p 00000000 00:00 0
7fce6ea28000-7fce6ea3e000 r-xp 00000000 00:23 37780346 /mnt/common/rh6/ngsdev/lib64/libgcc_s.so.1
7fce6ea3e000-7fce6ec3d000 ---p 00016000 00:23 37780346 /mnt/common/rh6/ngsdev/lib64/libgcc_s.so.1
7fce6ec3d000-7fce6ec3e000 rw-p 00015000 00:23 37780346 /mnt/common/rh6/ngsdev/lib64/libgcc_s.so.1
7fce6ec3e000-7fce6ecc1000 r-xp 00000000 fd:00 4116 /lib64/libm-2.12.so
7fce6ecc1000-7fce6eec0000 ---p 00083000 fd:00 4116 /lib64/libm-2.12.so
7fce6eec0000-7fce6eec1000 r--p 00082000 fd:00 4116 /lib64/libm-2.12.so
7fce6eec1000-7fce6eec2000 rw-p 00083000 fd:00 4116 /lib64/libm-2.12.so
7fce6eec2000-7fce6efb5000 r-xp 00000000 00:23 37781066 /mnt/common/rh6/ngsdev/lib64/libstdc++.so.6.0.20
7fce6efb5000-7fce6f1b4000 ---p 000f3000 00:23 37781066 /mnt/common/rh6/ngsdev/lib64/libstdc++.so.6.0.20
7fce6f1b4000-7fce6f1bd000 r--p 000f2000 00:23 37781066 /mnt/common/rh6/ngsdev/lib64/libstdc++.so.6.0.20
7fce6f1bd000-7fce6f1bf000 rw-p 000fb000 00:23 37781066 /mnt/common/rh6/ngsdev/lib64/libstdc++.so.6.0.20
7fce6f1bf000-7fce6f1d4000 rw-p 00000000 00:00 0
7fce6f1d4000-7fce6f1f4000 r-xp 00000000 fd:00 4101 /lib64/ld-2.12.so
7fce6f3da000-7fce6f3df000 rw-p 00000000 00:00 0
7fce6f3ef000-7fce6f3f3000 rw-p 00000000 00:00 0
7fce6f3f3000-7fce6f3f5000 r--p 0001f000 fd:00 4101 /lib64/ld-2.12.so
7fce6f3f5000-7fce6f3f6000 rw-p 00021000 fd:00 4101 /lib64/ld-2.12.so
7fce6f3f6000-7fce6f3f7000 rw-p 00000000 00:00 0
7ffc6c67c000-7ffc6c692000 rw-p 00000000 00:00 0 [stack]
7ffc6c790000-7ffc6c791000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)
Some more info from the standard error file:
[...]
sh: line 1: 3741 Aborted (core dumped) /ngsprod/gsap/tools/PASA_Dev/bin/pasa /anno/sanyalab/TEMP/pasa.1492343154-0.295204197828756.+.in > /anno/sanyalab/TEMP/pasa.1492343154-0.295204197828756.+.out
PASA died on input file. See pasa_killer.inputThread 3 terminated abnormally: Died at /ngsprod/gsap/tools/PASA_Dev/scripts/..//PerlLib//CDNA/PASA_alignment_assembler.pm line 262.
Thread(2) SUCCESS CMD: unknown Time to complete: 132206 seconds
ERROR, thread 3 exited with error Died at /ngsprod/gsap/tools/PASA_Dev/scripts/..//PerlLib//CDNA/PASA_alignment_assembler.pm line 262.
Thread(3) ERROR CMD: unknown Time to complete: 132206 seconds
Thread(4) SUCCESS CMD: unknown Time to complete: 132207 seconds
Thread(5) SUCCESS CMD: unknown Time to complete: 132207 seconds
Thread(6) SUCCESS CMD: unknown Time to complete: 132208 seconds
Thread(7) SUCCESS CMD: unknown Time to complete: 132208 seconds
Thread(8) SUCCESS CMD: unknown Time to complete: 132209 seconds
Thread(9) SUCCESS CMD: unknown Time to complete: 132209 seconds
Thread(10) SUCCESS CMD: unknown Time to complete: 132209 seconds
Thread(11) SUCCESS CMD: unknown Time to complete: 132210 seconds
Error, there were 1 threads (contig jobs) that failed... See error messages above in order to troubleshoot further at /ngsprod/gsap/tools/PASA_Dev/scripts/..//scripts/cDNA_annotation_comparer.dbi line 311.
Use of uninitialized value $index in concatenation (.) or string at /ngsprod/gsap/tools/PASA_Dev/scripts/Launch_PASA_pipeline.pl line 981.
Use of uninitialized value $index in concatenation (.) or string at /ngsprod/gsap/tools/PASA_Dev/scripts/Launch_PASA_pipeline.pl line 981.
ERROR: The following command died with exit code (6400):
/ngsprod/gsap/tools/PASA_Dev/scripts/..//scripts/cDNA_annotation_comparer.dbi -G /gsap/prod/data/gsap580/cleanfasta/gsap580.fa --CPU 12 -M gsap580 > pasa_run.log.dir/gsap580.annotation_compare.8058.out
Must re-run pipeline starting at index [] via running Launch_PASA_pipeline with parameter '-s ' (exclude param '-C' since db already created)
I'm unable to tell if it's a PASA issue, if its a data corruption issue or simply the server memory issue. Pleas advise. Your help is greatly appreciated!!
Thanks,
Guna
Brian Haas
Apr 18, 2017, 8:32:24 PM4/18/17
to Guna, pasapipeline-users
Hi Guna,
I wonder if you might need to recompile pasa. If you run
pasa pasa_killer.input
on a different server, does it still fail the same way?
If you want to send me your 'pasa_killer.input', I'd be happy to give it a look.
best,
~b
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Guna
Apr 18, 2017, 10:47:18 PM4/18/17
to pasapipeline-users, guna...@gmail.com, bh...@broadinstitute.org
Hi Brian,
Thanks for your response! That's a possibility, and I could try recompiling if you believe that might be the cause - why do you think? thanks for the suggestion.
Would you recommend this as your latest stable release? https://github.com/PASApipeline/PASApipeline/releases/tag/v2.1.0 I might need to update gmap anyway too.
I did try on a different server, and get the same failure. However, we could be using the same filesystem/binaries across different server, so not really a "different" pasa installation in the typical case.
Attached is my pasa_killer.input file, if you could give it a try - I would much appreciate it! (However I'm really perplexed how this works with just those couple of lines that you are able to verify w/o the actual data.. really cool!)
Thanks again,
Guna
Thanks for your response! That's a possibility, and I could try recompiling if you believe that might be the cause - why do you think? thanks for the suggestion.
Would you recommend this as your latest stable release? https://github.com/PASApipeline/PASApipeline/releases/tag/v2.1.0 I might need to update gmap anyway too.
I did try on a different server, and get the same failure. However, we could be using the same filesystem/binaries across different server, so not really a "different" pasa installation in the typical case.
Attached is my pasa_killer.input file, if you could give it a try - I would much appreciate it! (However I'm really perplexed how this works with just those couple of lines that you are able to verify w/o the actual data.. really cool!)
Thanks again,
Guna
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Brian Haas
Apr 19, 2017, 6:57:27 PM4/19/17
to Guna, pasapipeline-users
Hi Guna,
It looks like the 'evm.model.Chr02_genome_PacBio.4107' model has overlapping exons, which is causing a problem for the pasa assembler.
I see 'evm' in the model name... EVM shouldn't be generating models w/ overlapping exons. Did this model come from some other source?
~b
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Guna
Apr 20, 2017, 6:20:15 PM4/20/17
to pasapipeline-users, guna...@gmail.com, bh...@broadinstitute.org
Hi Brian,
That's an excellent insight! Now I realize how you read into these pasa_killer.input files. It is true that the preceding result/models come from EVM and it does indeed seem like the overlapping exons is causing the issue here and PASA to fail.
However, upon closer inspection, it seems that the overlapping exons are coming from the first iteration of pasa annotation. Usually, I realize that pasa updates appends overlapping models or isoforms with an ID or GUID as suffix, but in this particular case of 'evm.model.Chr02_genome_PacBio.4107' that did not happen, and hence pasa assembler fails in the second iteration. I've rerun the pasa annotation step and can recreate the exact failure. Do you know why this might have happened? Is there a workaround? I'm not sure if there might be other examples of such instances in the output of the first iteration - doesn't seem to be the case in my brief inspection at least.
See below order of events/steps, with excerpts from the related GFF files, and it'll make sense. I really hope you can help/advise to find a solution. Many thanks in advance! Again appreciate your time and interest in supporting the community.
$ <evm.gff3>
Chr02_genome_PacBio EVM gene 176085480 176088808 . - . ID=evm.TU.Chr02_genome_PacBio.4107;Name=EVM prediction Chr02_genome_PacBio.4107
Chr02_genome_PacBio EVM mRNA 176085480 176088808 . - . ID=evm.model.Chr02_genome_PacBio.4107;Parent=evm.TU.Chr02_genome_PacBio.4107
Chr02_genome_PacBio EVM exon 176088065 176088808 . - . ID=evm.model.Chr02_genome_PacBio.4107.exon1;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio EVM CDS 176088065 176088808 . - 0 ID=evm.model.Chr02_genome_PacBio.4107.cds1;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio EVM exon 176085707 176086585 . - . ID=evm.model.Chr02_genome_PacBio.4107.exon2;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio EVM CDS 176085707 176086585 . - 0 ID=evm.model.Chr02_genome_PacBio.4107.cds2;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio EVM exon 176085480 176085578 . - . ID=evm.model.Chr02_genome_PacBio.4107.exon3;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio EVM CDS 176085480 176085578 . - 0 ID=evm.model.Chr02_genome_PacBio.4107.cds3;Parent=evm.model.Chr02_genome_PacBio.4107
PASA Annotation begins...
working on iteration 1
/ngsprod/gsap/tools/PASA_Dev/scripts/Load_Current_Gene_Annotations.dbi -c pasa_align_assemble.config -g genome.fa -P evm.gff3
/ngsprod/gsap/tools/PASA_Dev/scripts/Launch_PASA_pipeline.pl -c pasa_annotation.config -A -g genome.fa -t ESTcDNA_PASA.fa.clean --CPU 12
the latest gff file in temp dir is gsap580.gene_structures_post_PASA_updates.31373.gff3
$ <gsap580.gene_structures_post_PASA_updates.31373.gff3>
# PASA_UPDATE: evm.model.Chr02_genome_PacBio.4107, single gene model update, valid-1, status:[pasa:asmbl_43989,status:40], valid-1
# PASA_UPDATE: evm.model.Chr02_genome_PacBio.4107, single gene model update, valid-1, status:[pasa:asmbl_43990,status:40], valid-1
Chr02_genome_PacBio . gene 176085462 176088997 . - . ID=evm.TU.Chr02_genome_PacBio.4107;Name=EVM%20prediction%20Chr02_genome_PacBio.4107
Chr02_genome_PacBio . mRNA 176085462 176088447 . - . ID=evm.model.Chr02_genome_PacBio.4107;Parent=evm.TU.Chr02_genome_PacBio.4107;Name=EVM%20prediction%20Chr02_genome_PacBio.4107
Chr02_genome_PacBio . five_prime_UTR 176088332 176088447 . - . ID=evm.model.Chr02_genome_PacBio.4107.utr5p1;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio . exon 176088065 176088447 . - . ID=evm.model.Chr02_genome_PacBio.4107.exon1;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio . CDS 176088065 176088331 . - 0 ID=cds.evm.model.Chr02_genome_PacBio.4107;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio . exon 176085462 176086585 . - . ID=evm.model.Chr02_genome_PacBio.4107.exon2;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio . CDS 176085656 176086585 . - 0 ID=cds.evm.model.Chr02_genome_PacBio.4107;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio . three_prime_UTR 176085462 176085655 . - . ID=evm.model.Chr02_genome_PacBio.4107.utr3p1;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio . mRNA 176087942 176088997 . - . ID=evm.model.Chr02_genome_PacBio.4107;Parent=evm.TU.Chr02_genome_PacBio.4107;Name=EVM%20prediction%20Chr02_genome_PacBio.4107
Chr02_genome_PacBio . five_prime_UTR 176088809 176088997 . - . ID=evm.model.Chr02_genome_PacBio.4107.utr5p1;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio . exon 176087942 176088997 . - . ID=evm.model.Chr02_genome_PacBio.4107.exon1;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio . CDS 176087999 176088808 . - 0 ID=cds.evm.model.Chr02_genome_PacBio.4107;Parent=evm.model.Chr02_genome_PacBio.4107
Chr02_genome_PacBio . three_prime_UTR 176087942 176087998 . - . ID=evm.model.Chr02_genome_PacBio.4107.utr3p1;Parent=evm.model.Chr02_genome_PacBio.4107
#PROT evm.model.Chr02_genome_PacBio.4107 evm.TU.Chr02_genome_PacBio.4107 [protein seq 1...]
#PROT evm.model.Chr02_genome_PacBio.4107 evm.TU.Chr02_genome_PacBio.4107 [protein seq 2...]
working on iteration 2
/ngsprod/gsap/tools/PASA_Dev/scripts/Load_Current_Gene_Annotations.dbi -c pasa_align_assemble.config -g genome.fa -P gsap580.gene_structures_post_PASA_updates.31373.gff3
/ngsprod/gsap/tools/PASA_Dev/scripts/Launch_PASA_pipeline.pl -c pasa_annotation.config -A -g genome.fa -t ESTcDNA_PASA.fa.clean --CPU 12
FAILED with core dump or memory error I posted earlier
$ cat pasa_killer.input
evm.model.Chr02_genome_PacBio.4107,-,176085462-176086585,176087942-176088997,176088065-176088447
asmbl_43989,-,176085462-176086585,176088065-176088447
If you are curious of the config files, please find them attached. Nothing much configured in there except for the MySQL db. Thanks
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Brian Haas
Apr 20, 2017, 8:43:14 PM4/20/17
to Guna, pasapipeline-users
Hi Guna,
Are you using the latest version of PASA? I'm just wondering if this is something I might have fixed in a later release.
In this particular case, it looks like there's supposed to be alt splicing going on, but the additional isoform wasn't given a unique identifier for some peculiar reason. If it's just this one gene that's giving you trouble, you might just delete the smaller isoform manually (removing it from the gff3 file used in the annotation comparison).
If there's a rare bug in there, I should aim to fix it at some point, but I haven't had time to do much w/ pasa as of late... to many other more pressing things going on. I would like to revisit it at some point though.
best,
~brian
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Guna
Apr 22, 2017, 2:04:22 PM4/22/17
to pasapipeline-users, guna...@gmail.com, bh...@broadinstitute.org
Hi Brian,
Thanks for your response again. I might not be running the very latest available at https://github.com/PASApipeline/PASApipeline/releases/tag/v2.1.0 for sure. So will update PASA to see if this bug might've been addressed.
However, for this particular case, since it's a time consuming process for the entire genome, I'll try the manual fix like you suggest (deleting the isoform) and re-run the 2nd iteration. Any idea how to restart the PASA pipeline even closer to the failure point? My logs suggest something as below, but there is no index# printed. However, thread 3 seems to have failed if that helps at all.
Thread(2) SUCCESS CMD: unknown Time to complete: 135560 seconds
ERROR, thread 3 exited with error Died at /ngsprod/gsap/tools/PASA_Dev/scripts/..//PerlLib//CDNA/PASA_alignment_assembler.pm line 262.
Thread(3) ERROR CMD: unknown Time to complete: 135560 seconds
Thread(4) SUCCESS CMD: unknown Time to complete: 135561 seconds
Thread(5) SUCCESS CMD: unknown Time to complete: 135562 seconds
Thread(6) SUCCESS CMD: unknown Time to complete: 135562 seconds
Thread(7) SUCCESS CMD: unknown Time to complete: 135563 seconds
Thread(8) SUCCESS CMD: unknown Time to complete: 135563 seconds
Thread(9) SUCCESS CMD: unknown Time to complete: 135564 seconds
Thread(10) SUCCESS CMD: unknown Time to complete: 135564 seconds
Thread(11) SUCCESS CMD: unknown Time to complete: 135563 seconds
Error, there were 1 threads (contig jobs) that failed... See error messages above in order to troubleshoot further at /ngsprod/gsap/tools/PASA_Dev/scripts/..//scripts/cDNA_annotation_comparer.dbi line 311.
Use of uninitialized value $index in concatenation (.) or string at /ngsprod/gsap/tools/PASA_Dev/scripts/Launch_PASA_pipeline.pl line 981.
Use of uninitialized value $index in concatenation (.) or string at /ngsprod/gsap/tools/PASA_Dev/scripts/Launch_PASA_pipeline.pl line 981.
ERROR: The following command died with exit code (6400):
/ngsprod/gsap/tools/PASA_Dev/scripts/..//scripts/cDNA_annotation_comparer.dbi -G /gsap/prod/data/gsap580/cleanfasta/gsap580.fa --CPU 12 -M gsap580 > pasa_run.log.dir/gsap580.annotation_compare.14409.out
Must re-run pipeline starting at index [] via running Launch_PASA_pipeline with parameter '-s ' (exclude param '-C' since db already created)
Finally, I completely understand other pressing priorities and the lack of time for continued support. Still your advises/responses on this forum are much appreciated and hugely helpful! Thanks again.
Best wishes,
Guna
p.s. A silly question, but have to ask... are you related to a certain Gene Haas by any chance? ;-P
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Brian Haas
Apr 22, 2017, 3:13:55 PM4/22/17
to Guna, pasapipeline-users
Hi Guna,
For the standard alignment assembly pipeline, you can resume at various stages, but for the annotation comparisons step, there isn't anything built in for resuming. Good luck w/ the manual edit and re-run.
Also, you're the 2nd person today to ask if I'm related to another Haas... popular German name, I guess. ;-) No relation to any Gene Haas, though.
best,
~b
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Guna Ranjan Gurazada
Apr 25, 2017, 7:07:51 PM4/25/17
to Brian Haas, pasapipeline-users
Thanks again Mr. Haas! ;-) Just wanted to let you know that that manual edit worked. It did seem to mess up some ID attributes for CDS features, model merges etc, but I fixed those too (not sure if PASA caused them or preceding EVM step).
Thanks for all your help. Will need to update to the latest version very soon though.
Cheers,
Guna
Brian Haas
Apr 25, 2017, 8:18:12 PM4/25/17
to Guna Ranjan Gurazada, pasapipeline-users
great! I'm glad it's working out for you.
best,
~b
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