Current state of cloudman etc. within private AWS VPCs?

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Chris Dagdigian

29 Jan 2016 29 Jan '16

4:51 p.m.

Apologies if this is asked often, I did a bit of searching and google-foo but could not find very new news...

I've long been a fan/user of cloudman-managed Galaxy clusters but for the first time I need galaxy in an AWS environment where we absolutely cannot stand up any sort of public facing service or any sort of host with a visible EIC IP address. The hosts can access the internet through NAT etc. but we can't run them in a public VPC or otherwise expose them to the Internet at large.

My experiment last night with cloudman launching inside a private VPC (with NAT'ed internet access and working forward/reverse DNS resolution for all hosts in the subnet) seemed to have failed - the key error in the cloudman logs was an endless iteration of "attempting to learn public hostname" log entries.

I blew away the install when I saw that error message endlessly repeating because there is zero chance our hosts in this VPC subnet will ever have a public FDQN hostname. They all have private IPs and private (but DNS resolvable) hostnames.

Can anyone give a current state update on cloudman inside private VPCs? Is this something I should have debugged further or am I better off just rolling my own AMI and installing galaxy and perhaps the cloudman elements by hand?

Thanks!

-Chris

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Enis Afgan

29 Jan 29 Jan

7:27 p.m.

New subject: Current state of cloudman etc. within private AWS VPCs?

Hi Chris, I believe you're the first person that's tried to run this in a completely private VPC so I don't have experience with it but can suggest a change that might get over this initial hump at least.

My guess is that get_galaxy_dns method is why you're seeing this log message ( https://github.com/galaxyproject/cloudman/blob/master/cm/controllers/root.py...) so perhaps changing that method to return an address you've configured as an accessible one would fix it? After changing the code, it'll also be necessary to update CloudMan source code in the corresponding bucket; see this page for more on that topic: https://wiki.galaxyproject.org/CloudMan/CustomizeGalaxyCloud#Using_custom_Cl...

Hope this helps. Let us know how things progress and we can update the code if a solution is generic.

Cheers, Enis

On Fri, Jan 29, 2016 at 10:51 AM, Chris Dagdigian dag@bioteam.net wrote:

...

Apologies if this is asked often, I did a bit of searching and google-foo but could not find very new news...

I've long been a fan/user of cloudman-managed Galaxy clusters but for the first time I need galaxy in an AWS environment where we absolutely cannot stand up any sort of public facing service or any sort of host with a visible EIC IP address. The hosts can access the internet through NAT etc. but we can't run them in a public VPC or otherwise expose them to the Internet at large.

My experiment last night with cloudman launching inside a private VPC (with NAT'ed internet access and working forward/reverse DNS resolution for all hosts in the subnet) seemed to have failed - the key error in the cloudman logs was an endless iteration of "attempting to learn public hostname" log entries.

I blew away the install when I saw that error message endlessly repeating because there is zero chance our hosts in this VPC subnet will ever have a public FDQN hostname. They all have private IPs and private (but DNS resolvable) hostnames.

Can anyone give a current state update on cloudman inside private VPCs? Is this something I should have debugged further or am I better off just rolling my own AMI and installing galaxy and perhaps the cloudman elements by hand?

Thanks!

-Chris

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Golhar, Ryan

7:48 p.m.

We are working in this as well and have something functioning. I'll leave it to Matt to give you the details as he's the one whose got it up and running.

Please excuse any typos -- Sent from my iPhone

On Jan 29, 2016, at 1:27 PM, Enis Afgan <enis.afgan@irb.hrmailto:enis.afgan@irb.hr> wrote:

My guess is that get_galaxy_dns method is why you're seeing this log message (https://github.com/galaxyproject/cloudman/blob/master/cm/controllers/root.py...) so perhaps changing that method to return an address you've configured as an accessible one would fix it? After changing the code, it'll also be necessary to update CloudMan source code in the corresponding bucket; see this page for more on that topic: https://wiki.galaxyproject.org/CloudMan/CustomizeGalaxyCloud#Using_custom_Cl...

Hope this helps. Let us know how things progress and we can update the code if a solution is generic.

Cheers, Enis

On Fri, Jan 29, 2016 at 10:51 AM, Chris Dagdigian <dag@bioteam.netmailto:dag@bioteam.net> wrote:

Apologies if this is asked often, I did a bit of searching and google-foo but could not find very new news...

Thanks!

-Chris

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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Makis Ladoukakis

31 Jan 31 Jan

6 p.m.

New subject: Error from Bowtie2 parser

Hello everyone,

I've built a bowtie2 parser for mapping reads back to contigs and while my Python parser works perfectly and even produces the files it's supposed too I get error files from Galaxy (and I've used 2>/dev/null at the end of the command). Even when I used Galaxy's job command line after the tool is finished the tool works but inside galaxy I get the following error:

*** Error in `python': double free or corruption ======= Backtrace: ========= /lib64/libc.so.6(+0x7d1fd)[0x7faab1c5d1fd] /lib64/libc.so.6(fclose+0x155)[0x7faab1c4bae5] /home/galaxy_coverall/galaxy/eggs/pysam-0.4.2_kanwei_b1 /home/galaxy_coverall/galaxy/eggs/pysam-0.4.2_kanwei_b1 /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7faab2 /lib64/libpython2.7.so.1.0(PyEval_CallObjectWithKeyword /home/galaxy_coverall/galaxy/eggs/pysam-0.4.2_kanwei_b1 /lib64/libpython2.7.so.1.0(+0x9fe13)[0x7faab297fe13] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7faab2 /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x1d4c)[0 /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x7 /lib64/libpython2.7.so.1.0(+0x6f17d)[0x7faab294f17d] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7faab2 /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xde7)[0x /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x4350)[0 /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x4350)[0 /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x7 /lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7faa /lib64/libpython2.7.so.1.0(+0xfb6cf)[0x7faab29db6cf] /lib64/libpython2.7.so.1.0(PyRun_FileExFlags+0x7e)[0x7f /lib64/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0xe9 /lib64/libpython2.7.so.1.0(Py_Main+0xc9f)[0x7faab29eeb1 /lib64/libc.so.6(__libc_start_main+0xf5)[0x7faab1c01af5 python[0x400721] ======= Memory map: ======== 00400000-00401000 r-xp 00000000 fd:00 134966341 00600000-00601000 r--p 00000000 fd:00 134966341 00601000-00602000 rw-p 00001000 fd:00 134966341 011a1000-064ce000 rw-p 00000000 00:00 0 7faaa15c8000-7faaa15dd000 r-xp 00000000 fd:00 205646465 7faaa15dd000-7faaa17dc000 ---p 00015000 fd:00 205646465 7faaa17dc000-7faaa17dd000 r--p 00014000 fd:00 205646465 7faaa17dd000-7faaa17de000 rw-p 00015000 fd:00 205646465 7faaa17e0000-7faaa1807000 r-xp 00000000 fd:00 201394264 7faaa1807000-7faaa1a07000 ---p 00027000 fd:00 201394264 7faaa1a07000-7faaa1a09000 r--p 00027000 fd:00 201394264 7faaa1a09000-7faaa1a0a000 rw-p 00029000 fd:00 201394264 7faaa1a10000-7faaa1a1b000 r-xp 00000000 fd:00 134861759 7faaa1a1b000-7faaa1c1a000 ---p 0000b000 fd:00 134861759 7faaa1c1a000-7faaa1c1b000 r--p 0000a000 fd:00 134861759 7faaa1c1b000-7faaa1c1d000 rw-p 0000b000 fd:00 134861759 7faaa1c20000-7faaa1c22000 r-xp 00000000 fd:02 423758729 7faaa1c22000-7faaa1d21000 ---p 00002000 fd:02 423758729 7faaa1d21000-7faaa1d22000 rw-p 00001000 fd:02 423758729 7faaa1d28000-7faaa1d32000 r-xp 00000000 fd:02 423758731 7faaa1d32000-7faaa1e32000 ---p 0000a000 fd:02 423758731 7faaa1e32000-7faaa1e33000 rw-p 0000a000 fd:02 423758731 7faaa1e38000-7faaa1e3a000 r-xp 00000000 fd:02 423758730 7faaa1e3a000-7faaa1f39000 ---p 00002000 fd:02 423758730 7faaa1f39000-7faaa1f3a000 rw-p 00001000 fd:02 423758730 7faaa1f40000-7faaa1f43000 r-xp 00000000 fd:02 423758728 7faaa1f43000-7faaa2042000 ---p 00003000 fd:02 423758728 7faaa2042000-7faaa2043000 rw-p 00002000 fd:02 423758728 7faaa2048000-7faaa204a000 r-xp 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r-xp 00000000 fd:02 9071725516 7faaa2796000-7faaa2895000 ---p 0000e000 fd:02 9071725516 7faaa2895000-7faaa2897000 rw-p 0000d000 fd:02 9071725516 7faaa2898000-7faaa28a0000 r-xp 00000000 fd:02 9071725515 7faaa28a0000-7faaa29a0000 ---p 00008000 fd:02 9071725515 7faaa29a0000-7faaa29a1000 rw-p 00008000 fd:02 9071725515 7faaa29a8000-7faaa29d3000 r-xp 00000000 fd:02 9071725517 7faaa29d3000-7faaa2ad3000 ---p 0002b000 fd:02 9071725517 7faaa2ad3000-7faaa2ad6000 rw-p 0002b000 fd:02 9071725517 7faaa2ad6000-7faaa2ad7000 rw-p 00000000 00:00 0 7faaa2ad8000-7faaa2ae6000 r-xp 00000000 fd:02 9071725519 7faaa2ae6000-7faaa2be6000 ---p 0000e000 fd:02 9071725519 7faaa2be6000-7faaa2be8000 rw-p 0000e000 fd:02 9071725519 7faaa2be8000-7faaa2be9000 rw-p 00000000 00:00 0 7faaa2bf0000-7faaa2bf7000 r-xp 00000000 fd:00 201393931 7faaa2bf7000-7faaa2df6000 ---p 00007000 fd:00 201393931 7faaa2df6000-7faaa2df7000 r--p 00006000 fd:00 201393931 7faaa2df7000-7faaa2df8000 rw-p 00007000 fd:00 201393931 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00003000 fd:02 9071725431 7faaa3458000-7faaa3467000 r-xp 00000000 fd:02 4675969882 7faaa3467000-7faaa3567000 ---p 0000f000 fd:02 4675969882 7faaa3567000-7faaa3569000 rw-p 0000f000 fd:02 4675969882 7faaa3570000-7faaa3584000 r-xp 00000000 fd:02 390174777 7faaa3584000-7faaa3683000 ---p 00014000 fd:02 390174777 7faaa3683000-7faaa3686000 rw-p 00013000 fd:02 390174777 7faaa3688000-7faaa36ce000 r-xp 00000000 fd:02 423758022 7faaa36ce000-7faaa37cd000 ---p 00046000 fd:02 423758022 7faaa37cd000-7faaa3802000 rw-p 00045000 fd:02 423758022 7faaa3802000-7faaa3803000 rw-p 00000000 00:00 0 7faaa3808000-7faaa3811000 r-xp 00000000 fd:02 423758008 7faaa3811000-7faaa3910000 ---p 00009000 fd:02 423758008 7fa .. /usr/lib64/libcom_err.so.2.1 7faaa82c3000-7faaa84c2000 ---p 00003000 fd:00 201394128 7faaa84c2000-7faaa84c3000 r--p 00002000 fd:00 201394128 7faaa84c3000-7faaa84c4000 rw-p 00003000 fd:00 201394128 7faaa84c8000-7faaa859b000 r-xp 00000000 fd:00 202456210 7faaa859b000-7faaa879b000 ---p 000d3000 fd:00 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7faab26c0000-7faab26d6000 r-xp 00000000 fd:00 201393927 7faab26d6000-7faab28d6000 ---p 00016000 fd:00 201393927 7faab28d6000-7faab28d7000 r--p 00016000 fd:00 201393927 7faab28d7000-7faab28d8000 rw-p 00017000 fd:00 201393927 7faab28d8000-7faab28dc000 rw-p 00000000 00:00 0 7faab28e0000-7faab2a58000 r-xp 00000000 fd:00 206021639 7faab2a58000-7faab2c58000 ---p 00178000 fd:00 206021639 7faab2c58000-7faab2c59000 r--p 00178000 fd:00 206021639 7faab2c59000-7faab2c97000 rw-p 00179000 fd:00 206021639 7faab2c97000-7faab2ca6000 rw-p 00000000 00:00 0 7faab2ca8000-7faab2cc9000 r-xp 00000000 fd:00 201393894 7faab2ccd000-7faab2e12000 rw-p 00000000 00:00 0 7faab2e41000-7faab2ec9000 rw-p 00000000 00:00 0 7faab2ec9000-7faab2eca000 r--p 00021000 fd:00 201393894 7faab2eca000-7faab2ecb000 rw-p 00022000 fd:00 201393894 7faab2ecb000-7faab2ecd000 rw-p 00000000 00:00 0 7faab2ecd000-7faab2ecf000 rw-p 00000000 00:00 0 7ffc473a7000-7ffc473c9000 rw-p 00000000 00:00 0 7ffc473e0000-7ffc473e2000 r-xp 00000000 00:00 0 ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 /home/galaxy_coverall/galaxy/database/job_working_direc My parser does the following: 1) Creates a sam file from an already indexed 2) Calls samtools to create the appropriate bam file 3) Calls samtools again to create the appropriate (!prev): 0x0000000002debfc0 *** 0f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(bam_index_load_literal+0x37)[0x7faaa43c2ad7] 0f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x6e7f8)[0x7faaa43ae7f8] 92a073] s+0x47)[0x7faab29bbfd7] 0f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x52a04)[0x7faaa4392a04] 92a073] x7faab29be32c] faab29c218d] 92a073] 7faab29bd3c7] x7faab29c0930] x7faab29c0930] faab29c218d] b29c2292] aab29dc88e] )[0x7faab29ddb19] f] ] /usr/bin/python2.7 /usr/bin/python2.7 /usr/bin/python2.7 [heap] /usr/lib64/libgcc_s-4.8.5-20150702.so.1 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 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/home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/mpatch.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/mpatch.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/bdiff.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/bdiff.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/bdiff.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/base85.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/base85.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/base85.so /usr/lib64/python2.7/lib-dynload/termios.so /usr/lib64/python2.7/lib-dynload/termios.so /usr/lib64/python2.7/lib-dynload/termios.so /usr/lib64/python2.7/lib-dynload/termios.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/osutil.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/osutil.so /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/osutil.so /usr/lib64/python2.7/lib-dynload/_multiprocessing.so /usr/lib64/python2.7/lib-dynload/_multiprocessing.so /usr/lib64/python2.7/lib-dynload/_multiprocessing.so /usr/lib64/python2.7/lib-dynload/_multiprocessing.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bigwig_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bigwig_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bigwig_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/cirtree_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/cirtree_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/cirtree_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bpt_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bpt_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bpt_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bbi_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bbi_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bbi_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bigbed_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bigbed_file.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bigbed_file.so /usr/lib64/librt-2.17.so /usr/lib64/librt-2.17.so /usr/lib64/librt-2.17.so /usr/lib64/librt-2.17.so /home/galaxy_coverall/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg/markupsafe/_speedups.so /home/galaxy_coverall/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg/markupsafe/_speedups.so /home/galaxy_coverall/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg/markupsafe/_speedups.so /home/galaxy_coverall/.python-eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg-tmp/Crypto/Cipher/Blowfish.so /home/galaxy_coverall/.python-eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg-tmp/Crypto/Cipher/Blowfish.so /home/galaxy_coverall/.python-eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg-tmp/Crypto/Cipher/Blowfish.so /home/galaxy_coverall/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/_namemapper.so /home/galaxy_coverall/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/_namemapper.so /home/galaxy_coverall/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/_namemapper.so /home/galaxy_coverall/.python-eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg-tmp/lzo.so /home/galaxy_coverall/.python-eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg-tmp/lzo.so /home/galaxy_coverall/.python-eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg-tmp/lzo.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/misc/_seekbzip2.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/misc/_seekbzip2.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/misc/_seekbzip2.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/align/_core.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/align/_core.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/align/_core.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bitset.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bitset.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bitset.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/intervals/intersection.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/intervals/intersection.so /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/intervals/intersection.so /home/galaxy_coverall/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg/numpy/random/mtrand.so /home/galaxy_coverall/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg/numpy/random/mtrand.so /home/galaxy_coverall/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg/numpy/random/mtrand.so /home/galaxy_coverall/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg/numpy/fft/fftpack_lite.so /home/galaxy_coverall/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg/numpy/fft/fftpack_lite.so /usr/lib64/libcom_err.so.2.1 /usr/lib64/libcom_err.so.2.1 /usr/lib64/libcom_err.so.2.1 /usr/lib64/libkrb5.so.3.3 /usr/lib64/libkrb5.so.3.3 /usr/lib64/libkrb5.so.3.3 /usr/lib64/libkrb5.so.3.3 /usr/lib64/libgssapi_krb5.so.2.2 /usr/lib64/libgssapi_krb5.so.2.2 /usr/lib64/libgssapi_krb5.so.2.2 /usr/lib64/libgssapi_krb5.so.2.2 /usr/lib64/libcrypto.so.1.0.1e /usr/lib64/libcrypto.so.1.0.1e /usr/lib64/libcrypto.so.1.0.1e /usr/lib64/libcrypto.so.1.0.1e /usr/lib64/libssl.so.1.0.1e /usr/lib64/libssl.so.1.0.1e /usr/lib64/libssl.so.1.0.1e /usr/lib64/libssl.so.1.0.1e /usr/lib64/python2.7/lib-dynload/_ssl.so /usr/lib64/python2.7/lib-dynload/_ssl.so /usr/lib64/python2.7/lib-dynload/_ssl.so /usr/lib64/python2.7/lib-dynload/_ssl.so /usr/lib64/python2.7/lib-dynload/_functoolsmodule.so /usr/lib64/python2.7/lib-dynload/_functoolsmodule.so /usr/lib64/python2.7/lib-dynload/_functoolsmodule.so /usr/lib64/python2.7/lib-dynload/_functoolsmodule.so /usr/lib64/python2.7/lib-dynload/_socketmodule.so /usr/lib64/python2.7/lib-dynload/_socketmodule.so /usr/lib64/python2.7/lib-dynload/_socketmodule.so /usr/lib64/python2.7/lib-dynload/_socketmodule.so /usr/lib64/libz.so.1.2.7 /usr/lib64/libz.so.1.2.7 /usr/lib64/libz.so.1.2.7 /usr/lib64/libz.so.1.2.7 /usr/lib64/python2.7/lib-dynload/zlibmodule.so /usr/lib64/python2.7/lib-dynload/zlibmodule.so /usr/lib64/python2.7/lib-dynload/zlibmodule.so /usr/lib64/python2.7/lib-dynload/zlibmodule.so /usr/lib64/python2.7/lib-dynload/_io.so /usr/lib64/python2.7/lib-dynload/_io.so /usr/lib64/python2.7/lib-dynload/_io.so /usr/lib64/python2.7/lib-dynload/_io.so /usr/lib64/python2.7/lib-dynload/grpmodule.so /usr/lib64/python2.7/lib-dynload/grpmodule.so /usr/lib64/python2.7/lib-dynload/grpmodule.so /usr/lib64/python2.7/lib-dynload/grpmodule.so /usr/lib64/python2.7/lib-dynload/stropmodule.so /usr/lib64/python2.7/lib-dynload/stropmodule.so /usr/lib64/python2.7/lib-dynload/stropmodule.so /usr/lib64/python2.7/lib-dynload/stropmodule.so /usr/lib64/python2.7/lib-dynload/_heapq.so /usr/lib64/python2.7/lib-dynload/_heapq.so /usr/lib64/python2.7/lib-dynload/_heapq.so /usr/lib64/python2.7/lib-dynload/_heapq.so /usr/lib64/python2.7/lib-dynload/itertoolsmodule.so /usr/lib64/python2.7/lib-dynload/itertoolsmodule.so /usr/lib64/python2.7/lib-dynload/itertoolsmodule.so /usr/lib64/python2.7/lib-dynload/itertoolsmodule.so /usr/lib64/python2.7/lib-dynload/operator.so /usr/lib64/python2.7/lib-dynload/operator.so /usr/lib64/python2.7/lib-dynload/operator.so /usr/lib64/python2.7/lib-dynload/operator.so /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so /usr/lib64/python2.7/lib-dynload/timemodule.so /usr/lib64/python2.7/lib-dynload/timemodule.so /usr/lib64/python2.7/lib-dynload/timemodule.so /usr/lib64/python2.7/lib-dynload/timemodule.so /usr/lib64/python2.7/lib-dynload/binascii.so /usr/lib64/python2.7/lib-dynload/binascii.so /usr/lib64/python2.7/lib-dynload/binascii.so /usr/lib64/python2.7/lib-dynload/binascii.so /usr/lib64/python2.7/lib-dynload/_json.so /usr/lib64/python2.7/lib-dynload/_json.so /usr/lib64/python2.7/lib-dynload/_json.so /usr/lib64/python2.7/lib-dynload/_json.so /usr/lib64/python2.7/lib-dynload/_struct.so /usr/lib64/python2.7/lib-dynload/_struct.so /usr/lib64/python2.7/lib-dynload/_struct.so /usr/lib64/python2.7/lib-dynload/_struct.so /usr/lib64/python2.7/lib-dynload/cStringIO.so /usr/lib64/python2.7/lib-dynload/cStringIO.so /usr/lib64/python2.7/lib-dynload/cStringIO.so /usr/lib64/python2.7/lib-dynload/cStringIO.so /usr/lib64/python2.7/lib-dynload/cPickle.so /usr/lib64/python2.7/lib-dynload/cPickle.so /usr/lib64/python2.7/lib-dynload/cPickle.so /usr/lib64/python2.7/lib-dynload/cPickle.so /usr/lib/locale/locale-archive /usr/lib64/libc-2.17.so /usr/lib64/libc-2.17.so /usr/lib64/libc-2.17.so /usr/lib64/libc-2.17.so /usr/lib64/libm-2.17.so /usr/lib64/libm-2.17.so /usr/lib64/libm-2.17.so /usr/lib64/libm-2.17.so /usr/lib64/libutil-2.17.so /usr/lib64/libutil-2.17.so /usr/lib64/libutil-2.17.so /usr/lib64/libutil-2.17.so /usr/lib64/libdl-2.17.so /usr/lib64/libdl-2.17.so /usr/lib64/libdl-2.17.so /usr/lib64/libdl-2.17.so /usr/lib64/libpthread-2.17.so /usr/lib64/libpthread-2.17.so /usr/lib64/libpthread-2.17.so /usr/lib64/libpthread-2.17.so /usr/lib64/libpython2.7.so.1.0 /usr/lib64/libpython2.7.so.1.0 /usr/lib64/libpython2.7.so.1.0 /usr/lib64/libpython2.7.so.1.0 /usr/lib64/ld-2.17.so /usr/lib64/ld-2.17.so /usr/lib64/ld-2.17.so [stack] [vdso] [vsyscall] tory2/000/30/galaxy_30.sh: line 21: 38559 Aborted (core dumped) python "/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/set_metadata_CkVy0K.py" "/home/galaxy_coverall/galaxy/database/tmp/tmpKjfqUF" "/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/galaxy.json" "/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_in_HistoryDatasetAssociation_49_0OTW3F,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_kwds_HistoryDatasetAssociation_49_HjgVuR,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_out_HistoryDatasetAssociation_49_on8AdF,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_results_HistoryDatasetAssociation_49_CnZVLx,/home/galaxy_coverall/galaxy/database/files2/001/dataset_1739.dat,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_override_HistoryDatasetAssociation_49_KSfIN1" "/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_in_HistoryDatasetAssociation_50_hwtfVm,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_kwds_HistoryDatasetAssociation_50_h1vk_m,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_out_HistoryDatasetAssociation_50_nT4xXj,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_results_HistoryDatasetAssociation_50_KaNi5o,/home/galaxy_coverall/galaxy/database/files2/001/dataset_1740.dat,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_override_HistoryDatasetAssociation_50_CHPwpR" "/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_in_HistoryDatasetAssociation_51_qFch9V,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_kwds_HistoryDatasetAssociation_51__ijkKo,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_out_HistoryDatasetAssociation_51_zvlnQn,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_results_HistoryDatasetAssociation_51_UhLJnu,/home/galaxy_coverall/galaxy/database/files2/001/dataset_1741.dat,/home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/metadata_override_HistoryDatasetAssociation_51_4t9S_g" 5242880 contig file sorted bam file

I've commented the steps one by one and the problem starts at the mapping (even though the scripts does continue to work and produces the files it's supposed too in the 'database/files/' directory)

Has anyone encountered something like that before?

Kind regards, Makis Ladoukakis

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participants (4)

Chris Dagdigian
Enis Afgan
Golhar, Ryan
Makis Ladoukakis