Current state of cloudman etc. within private AWS VPCs?
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
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
___________________________________________________________ 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/
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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.hr<mailto:enis.afgan@irb.hr>> wrote: 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<mailto: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 ___________________________________________________________ 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/ ___________________________________________________________ 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/ ________________________________ This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.
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 (!prev): 0x0000000002debfc0 *** ======= Backtrace: ========= /lib64/libc.so.6(+0x7d1fd)[0x7faab1c5d1fd] /lib64/libc.so.6(fclose+0x155)[0x7faab1c4bae5] /home/galaxy_coverall/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(bam_index_load_literal+0x37)[0x7faaa43c2ad7] /home/galaxy_coverall/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x6e7f8)[0x7faaa43ae7f8] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7faab292a073] /lib64/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47)[0x7faab29bbfd7] /home/galaxy_coverall/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x52a04)[0x7faaa4392a04] /lib64/libpython2.7.so.1.0(+0x9fe13)[0x7faab297fe13] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7faab292a073] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x1d4c)[0x7faab29be32c] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x7faab29c218d] /lib64/libpython2.7.so.1.0(+0x6f17d)[0x7faab294f17d] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7faab292a073] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xde7)[0x7faab29bd3c7] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x4350)[0x7faab29c0930] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x4350)[0x7faab29c0930] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x7faab29c218d] /lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7faab29c2292] /lib64/libpython2.7.so.1.0(+0xfb6cf)[0x7faab29db6cf] /lib64/libpython2.7.so.1.0(PyRun_FileExFlags+0x7e)[0x7faab29dc88e] /lib64/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0xe9)[0x7faab29ddb19] /lib64/libpython2.7.so.1.0(Py_Main+0xc9f)[0x7faab29eeb1f] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7faab1c01af5] python[0x400721] ======= Memory map: ======== 00400000-00401000 r-xp 00000000 fd:00 134966341 /usr/bin/python2.7 00600000-00601000 r--p 00000000 fd:00 134966341 /usr/bin/python2.7 00601000-00602000 rw-p 00001000 fd:00 134966341 /usr/bin/python2.7 011a1000-064ce000 rw-p 00000000 00:00 0 [heap] 7faaa15c8000-7faaa15dd000 r-xp 00000000 fd:00 205646465 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7faaa15dd000-7faaa17dc000 ---p 00015000 fd:00 205646465 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7faaa17dc000-7faaa17dd000 r--p 00014000 fd:00 205646465 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7faaa17dd000-7faaa17de000 rw-p 00015000 fd:00 205646465 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7faaa17e0000-7faaa1807000 r-xp 00000000 fd:00 201394264 /usr/lib64/libexpat.so.1.6.0 7faaa1807000-7faaa1a07000 ---p 00027000 fd:00 201394264 /usr/lib64/libexpat.so.1.6.0 7faaa1a07000-7faaa1a09000 r--p 00027000 fd:00 201394264 /usr/lib64/libexpat.so.1.6.0 7faaa1a09000-7faaa1a0a000 rw-p 00029000 fd:00 201394264 /usr/lib64/libexpat.so.1.6.0 7faaa1a10000-7faaa1a1b000 r-xp 00000000 fd:00 134861759 /usr/lib64/python2.7/lib-dynload/pyexpat.so 7faaa1a1b000-7faaa1c1a000 ---p 0000b000 fd:00 134861759 /usr/lib64/python2.7/lib-dynload/pyexpat.so 7faaa1c1a000-7faaa1c1b000 r--p 0000a000 fd:00 134861759 /usr/lib64/python2.7/lib-dynload/pyexpat.so 7faaa1c1b000-7faaa1c1d000 rw-p 0000b000 fd:00 134861759 /usr/lib64/python2.7/lib-dynload/pyexpat.so 7faaa1c20000-7faaa1c22000 r-xp 00000000 fd:02 423758729 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/diffhelpers.so 7faaa1c22000-7faaa1d21000 ---p 00002000 fd:02 423758729 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/diffhelpers.so 7faaa1d21000-7faaa1d22000 rw-p 00001000 fd:02 423758729 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/diffhelpers.so 7faaa1d28000-7faaa1d32000 r-xp 00000000 fd:02 423758731 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/parsers.so 7faaa1d32000-7faaa1e32000 ---p 0000a000 fd:02 423758731 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/parsers.so 7faaa1e32000-7faaa1e33000 rw-p 0000a000 fd:02 423758731 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/parsers.so 7faaa1e38000-7faaa1e3a000 r-xp 00000000 fd:02 423758730 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/mpatch.so 7faaa1e3a000-7faaa1f39000 ---p 00002000 fd:02 423758730 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/mpatch.so 7faaa1f39000-7faaa1f3a000 rw-p 00001000 fd:02 423758730 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/mpatch.so 7faaa1f40000-7faaa1f43000 r-xp 00000000 fd:02 423758728 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/bdiff.so 7faaa1f43000-7faaa2042000 ---p 00003000 fd:02 423758728 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/bdiff.so 7faaa2042000-7faaa2043000 rw-p 00002000 fd:02 423758728 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/bdiff.so 7faaa2048000-7faaa204a000 r-xp 00000000 fd:02 423758727 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/base85.so 7faaa204a000-7faaa2149000 ---p 00002000 fd:02 423758727 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/base85.so 7faaa2149000-7faaa214a000 rw-p 00001000 fd:02 423758727 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/base85.so 7faaa2150000-7faaa2154000 r-xp 00000000 fd:00 134861771 /usr/lib64/python2.7/lib-dynload/termios.so 7faaa2154000-7faaa2353000 ---p 00004000 fd:00 134861771 /usr/lib64/python2.7/lib-dynload/termios.so 7faaa2353000-7faaa2354000 r--p 00003000 fd:00 134861771 /usr/lib64/python2.7/lib-dynload/termios.so 7faaa2354000-7faaa2356000 rw-p 00004000 fd:00 134861771 /usr/lib64/python2.7/lib-dynload/termios.so 7faaa2358000-7faaa235a000 r-xp 00000000 fd:02 423758732 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/osutil.so 7faaa235a000-7faaa245a000 ---p 00002000 fd:02 423758732 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/osutil.so 7faaa245a000-7faaa245b000 rw-p 00002000 fd:02 423758732 /home/galaxy_coverall/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg/mercurial/osutil.so 7faaa2460000-7faaa2466000 r-xp 00000000 fd:00 137235630 /usr/lib64/python2.7/lib-dynload/_multiprocessing.so 7faaa2466000-7faaa2665000 ---p 00006000 fd:00 137235630 /usr/lib64/python2.7/lib-dynload/_multiprocessing.so 7faaa2665000-7faaa2666000 r--p 00005000 fd:00 137235630 /usr/lib64/python2.7/lib-dynload/_multiprocessing.so 7faaa2666000-7faaa2667000 rw-p 00006000 fd:00 137235630 /usr/lib64/python2.7/lib-dynload/_multiprocessing.so 7faaa2668000-7faaa267f000 r-xp 00000000 fd:02 9071725518 /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bigwig_file.so 7faaa267f000-7faaa277f000 ---p 00017000 fd:02 9071725518 /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bigwig_file.so 7faaa277f000-7faaa2781000 rw-p 00017000 fd:02 9071725518 /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bigwig_file.so 7faaa2781000-7faaa2782000 rw-p 00000000 00:00 0 7faaa2788000-7faaa2796000 r-xp 00000000 fd:02 9071725516 /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/cirtree_file.so 7faaa2796000-7faaa2895000 ---p 0000e000 fd:02 9071725516 /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/cirtree_file.so 7faaa2895000-7faaa2897000 rw-p 0000d000 fd:02 9071725516 /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/cirtree_file.so 7faaa2898000-7faaa28a0000 r-xp 00000000 fd:02 9071725515 /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bpt_file.so 7faaa28a0000-7faaa29a0000 ---p 00008000 fd:02 9071725515 /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bpt_file.so 7faaa29a0000-7faaa29a1000 rw-p 00008000 fd:02 9071725515 /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bpt_file.so 7faaa29a8000-7faaa29d3000 r-xp 00000000 fd:02 9071725517 /home/galaxy_coverall/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bbi_file.so 7faaa29d3000-7faaa2ad3000 ---p 0002b000 fd:02 9071725517 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7faaa9ddc000-7faaa9de6000 rw-p 0001c000 fd:00 137235625 /usr/lib64/python2.7/lib-dynload/_io.so 7faaa9de8000-7faaa9dea000 r-xp 00000000 fd:00 134861735 /usr/lib64/python2.7/lib-dynload/grpmodule.so 7faaa9dea000-7faaa9fe9000 ---p 00002000 fd:00 134861735 /usr/lib64/python2.7/lib-dynload/grpmodule.so 7faaa9fe9000-7faaa9fea000 r--p 00001000 fd:00 134861735 /usr/lib64/python2.7/lib-dynload/grpmodule.so 7faaa9fea000-7faaa9feb000 rw-p 00002000 fd:00 134861735 /usr/lib64/python2.7/lib-dynload/grpmodule.so 7faaa9fef000-7faaaa030000 rw-p 00000000 00:00 0 7faaaa030000-7faaaa035000 r-xp 00000000 fd:00 134861768 /usr/lib64/python2.7/lib-dynload/stropmodule.so 7faaaa035000-7faaaa234000 ---p 00005000 fd:00 134861768 /usr/lib64/python2.7/lib-dynload/stropmodule.so 7faaaa234000-7faaaa235000 r--p 00004000 fd:00 134861768 /usr/lib64/python2.7/lib-dynload/stropmodule.so 7faaaa235000-7faaaa237000 rw-p 00005000 fd:00 134861768 /usr/lib64/python2.7/lib-dynload/stropmodule.so 7faaaa238000-7faaaa23b000 r-xp 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7faaaa858000-7faaaa859000 r--p 00008000 fd:00 134861755 /usr/lib64/python2.7/lib-dynload/operator.so 7faaaa859000-7faaaa85b000 rw-p 00009000 fd:00 134861755 /usr/lib64/python2.7/lib-dynload/operator.so 7faaaa860000-7faaaa866000 r-xp 00000000 fd:00 134861692 /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so 7faaaa866000-7faaaaa65000 ---p 00006000 fd:00 134861692 /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so 7faaaaa65000-7faaaaa66000 r--p 00005000 fd:00 134861692 /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so 7faaaaa66000-7faaaaa68000 rw-p 00006000 fd:00 134861692 /usr/lib64/python2.7/lib-dynload/_collectionsmodule.so 7faaaaa68000-7faaaaa6c000 r-xp 00000000 fd:00 134861772 /usr/lib64/python2.7/lib-dynload/timemodule.so 7faaaaa6c000-7faaaac6b000 ---p 00004000 fd:00 134861772 /usr/lib64/python2.7/lib-dynload/timemodule.so 7faaaac6b000-7faaaac6c000 r--p 00003000 fd:00 134861772 /usr/lib64/python2.7/lib-dynload/timemodule.so 7faaaac6c000-7faaaac6e000 rw-p 00004000 fd:00 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/usr/lib64/libutil-2.17.so 7faab24b1000-7faab24b2000 r--p 00001000 fd:00 201393935 /usr/lib64/libutil-2.17.so 7faab24b2000-7faab24b3000 rw-p 00002000 fd:00 201393935 /usr/lib64/libutil-2.17.so 7faab24b8000-7faab24bb000 r-xp 00000000 fd:00 201393907 /usr/lib64/libdl-2.17.so 7faab24bb000-7faab26ba000 ---p 00003000 fd:00 201393907 /usr/lib64/libdl-2.17.so 7faab26ba000-7faab26bb000 r--p 00002000 fd:00 201393907 /usr/lib64/libdl-2.17.so 7faab26bb000-7faab26bc000 rw-p 00003000 fd:00 201393907 /usr/lib64/libdl-2.17.so 7faab26c0000-7faab26d6000 r-xp 00000000 fd:00 201393927 /usr/lib64/libpthread-2.17.so 7faab26d6000-7faab28d6000 ---p 00016000 fd:00 201393927 /usr/lib64/libpthread-2.17.so 7faab28d6000-7faab28d7000 r--p 00016000 fd:00 201393927 /usr/lib64/libpthread-2.17.so 7faab28d7000-7faab28d8000 rw-p 00017000 fd:00 201393927 /usr/lib64/libpthread-2.17.so 7faab28d8000-7faab28dc000 rw-p 00000000 00:00 0 7faab28e0000-7faab2a58000 r-xp 00000000 fd:00 206021639 /usr/lib64/libpython2.7.so.1.0 7faab2a58000-7faab2c58000 ---p 00178000 fd:00 206021639 /usr/lib64/libpython2.7.so.1.0 7faab2c58000-7faab2c59000 r--p 00178000 fd:00 206021639 /usr/lib64/libpython2.7.so.1.0 7faab2c59000-7faab2c97000 rw-p 00179000 fd:00 206021639 /usr/lib64/libpython2.7.so.1.0 7faab2c97000-7faab2ca6000 rw-p 00000000 00:00 0 7faab2ca8000-7faab2cc9000 r-xp 00000000 fd:00 201393894 /usr/lib64/ld-2.17.so 7faab2ccd000-7faab2e12000 rw-p 00000000 00:00 0 7faab2e41000-7faab2ec9000 rw-p 00000000 00:00 0 7faab2ec9000-7faab2eca000 r--p 00021000 fd:00 201393894 /usr/lib64/ld-2.17.so 7faab2eca000-7faab2ecb000 rw-p 00022000 fd:00 201393894 /usr/lib64/ld-2.17.so 7faab2ecb000-7faab2ecd000 rw-p 00000000 00:00 0 7faab2ecd000-7faab2ecf000 rw-p 00000000 00:00 0 7ffc473a7000-7ffc473c9000 rw-p 00000000 00:00 0 [stack] 7ffc473e0000-7ffc473e2000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] /home/galaxy_coverall/galaxy/database/job_working_directory2/000/30/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 My parser does the following: 1) Creates a sam file from an already indexed contig file 2) Calls samtools to create the appropriate bam file 3) Calls samtools again to create the appropriate 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
participants (4)
-
Chris Dagdigian -
Enis Afgan -
Golhar, Ryan -
Makis Ladoukakis