search

oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
337 stars 73 forks source link

OSError: /lib/x86_64-linux-gnu/libjemalloc.so.2: cannot allocate memory in static TLS block! #257

Closed cheehowteo closed 2 years ago

cheehowteo commented 2 years ago

Hi Shujun,

I encountered these problems when I try to run EDTA:

Traceback (most recent call last): File "/home/umcentral18/miniconda3/envs/EDTA/bin/TEsorter", line 6, in from TEsorter.app import main File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/TEsorter/app.py", line 25, in from .modules.RunCmdsMP import run_cmd, pp_run File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/TEsorter/modules/RunCmdsMP.py", line 20, in import drmaa # for grid File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/init.py", line 65, in from .session import JobInfo, JobTemplate, Session File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/session.py", line 39, in from drmaa.helpers import (adapt_rusage, Attribute, attribute_names_iterator, File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/helpers.py", line 36, in from drmaa.wrappers import (drmaa_attr_names_t, drmaa_attr_values_t, File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/wrappers.py", line 56, in _lib = CDLL(libpath, mode=RTLD_GLOBAL) File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/ctypes/init.py", line 348, in init self._handle = _dlopen(self._name, mode) OSError: /lib/x86_64-linux-gnu/libjemalloc.so.2: cannot allocate memory in static TLS block

Input not found! perl rename_RMTE.pl RM*/consensi.fa.classified > RepeatModeler.TE.raw.fa at /home/umcentral18/Downloads/EDTA/util/rename_RM_TE.pl line 29.

Input file "MR219.NB_rice7.fasta.mod.RepeatModeler.raw.fa.masked" not found!

    Usage: perl cleanup_tandem.pl -f sample.fa [options] > sample.cln.fa 
Options:
    -misschar   [n|l]   Define the letter representing unknown sequences; default: n. l: recognize lower case letters
    -Nscreen    [0|1]   Enable (1) or disable (0) the -nc parameter; default: 1
    -nc     [int]   Ambuguous sequence len cutoff; discard the entire sequence if > this number; default: 0
    -nr     [0-1]   Ambuguous sequence percentage cutoff; discard the entire sequence if > this number; default: 1
    -minlen     [int]   Minimum sequence length filter after clean up; default: 100 (bp)
    -maxlen     [int]   Maximum sequence length filter after clean up; default: 25000 (bp)
    -cleanN     [0|1]   Retain (0) or remove (1) the -misschar taget in output sequence; default: 0
    -cleanT     [0|1]   Remove entire seq. if any terminal seq (20bp) has 15bp of N (1); disabled by default (0).
    -minrm      [int]   The minimum length of -misschar to be removed if -cleanN 1; default: 1.
    -trf        [0|1]   Enable (1) or disable (0) tandem repeat finder (trf); default: 1
    -trf_path   path    Path to the trf program

Traceback (most recent call last): File "/home/umcentral18/miniconda3/envs/EDTA/bin/TEsorter", line 6, in from TEsorter.app import main File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/TEsorter/app.py", line 25, in from .modules.RunCmdsMP import run_cmd, pp_run File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/TEsorter/modules/RunCmdsMP.py", line 20, in import drmaa # for grid File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/init.py", line 65, in from .session import JobInfo, JobTemplate, Session File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/session.py", line 39, in from drmaa.helpers import (adapt_rusage, Attribute, attribute_names_iterator, File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/helpers.py", line 36, in from drmaa.wrappers import (drmaa_attr_names_t, drmaa_attr_values_t, File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/wrappers.py", line 56, in _lib = CDLL(libpath, mode=RTLD_GLOBAL) File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/ctypes/init.py", line 348, in init self._handle = _dlopen(self._name, mode) OSError: /lib/x86_64-linux-gnu/libjemalloc.so.2: cannot allocate memory in static TLS block cat: Oryza_sativa.IRGSP-1.0.cds.all.fa.code.rexdb.cls.tsv: No such file or directory

May I know how can I fix this?

Thank you.

Best regards, Teo

oushujun commented 2 years ago

Hi Teo,

Please reinstall EDTA and test it with the small data.

Shujun

On Wed, Mar 2, 2022 at 2:32 AM cheehowteo @.***> wrote:

Hi Shujun,

I encountered these problems when I try to run EDTA:

Traceback (most recent call last): File "/home/umcentral18/miniconda3/envs/EDTA/bin/TEsorter", line 6, in from TEsorter.app import main File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/TEsorter/app.py", line 25, in from .modules.RunCmdsMP import run_cmd, pp_run File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/TEsorter/modules/RunCmdsMP.py", line 20, in import drmaa # for grid File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/ init.py", line 65, in from .session import JobInfo, JobTemplate, Session File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/session.py", line 39, in from drmaa.helpers import (adapt_rusage, Attribute, attribute_names_iterator, File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/helpers.py", line 36, in from drmaa.wrappers import (drmaa_attr_names_t, drmaa_attr_values_t, File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/wrappers.py", line 56, in _lib = CDLL(libpath, mode=RTLD_GLOBAL) File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/ctypes/init.py", line 348, in init self._handle = _dlopen(self._name, mode) OSError: /lib/x86_64-linux-gnu/libjemalloc.so.2: cannot allocate memory in static TLS block

Input not found! perl rename_RMTE.pl RM*/consensi.fa.classified > RepeatModeler.TE.raw.fa at /home/umcentral18/Downloads/EDTA/util/rename_RM_TE.pl line 29.

Input file "MR219.NB_rice7.fasta.mod.RepeatModeler.raw.fa.masked" not found!

Usage: perl cleanup_tandem.pl -f sample.fa [options] > sample.cln.fa

Options: -misschar [n|l] Define the letter representing unknown sequences; default: n. l: recognize lower case letters -Nscreen [0|1] Enable (1) or disable (0) the -nc parameter; default: 1 -nc [int] Ambuguous sequence len cutoff; discard the entire sequence if > this number; default: 0 -nr [0-1] Ambuguous sequence percentage cutoff; discard the entire sequence if > this number; default: 1 -minlen [int] Minimum sequence length filter after clean up; default: 100 (bp) -maxlen [int] Maximum sequence length filter after clean up; default: 25000 (bp) -cleanN [0|1] Retain (0) or remove (1) the -misschar taget in output sequence; default: 0 -cleanT [0|1] Remove entire seq. if any terminal seq (20bp) has 15bp of N (1); disabled by default (0). -minrm [int] The minimum length of -misschar to be removed if -cleanN 1; default: 1. -trf [0|1] Enable (1) or disable (0) tandem repeat finder (trf); default: 1 -trf_path path Path to the trf program

Traceback (most recent call last): File "/home/umcentral18/miniconda3/envs/EDTA/bin/TEsorter", line 6, in from TEsorter.app import main File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/TEsorter/app.py", line 25, in from .modules.RunCmdsMP import run_cmd, pp_run File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/TEsorter/modules/RunCmdsMP.py", line 20, in import drmaa # for grid File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/ init.py", line 65, in from .session import JobInfo, JobTemplate, Session File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/session.py", line 39, in from drmaa.helpers import (adapt_rusage, Attribute, attribute_names_iterator, File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/helpers.py", line 36, in from drmaa.wrappers import (drmaa_attr_names_t, drmaa_attr_values_t, File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/drmaa/wrappers.py", line 56, in _lib = CDLL(libpath, mode=RTLD_GLOBAL) File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/ctypes/init.py", line 348, in init self._handle = _dlopen(self._name, mode) OSError: /lib/x86_64-linux-gnu/libjemalloc.so.2: cannot allocate memory in static TLS block cat: Oryza_sativa.IRGSP-1.0.cds.all.fa.code.rexdb.cls.tsv: No such file or directory

May I know how can I fix this?

Thank you.

Best regards, Teo

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/257, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NGXYGXLOC75IDZBCTDU54KPFANCNFSM5PWQ47XQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

oushujun commented 2 years ago

@cheehowteo any luck?

cheehowteo commented 1 year ago

Dear Ou,

I tried to reinstall the EDTA but I still obtained the same error message.

Thank you.

Best regards, Teo

On Wed, Apr 6, 2022 at 3:13 PM Shujun Ou @.***> wrote:

@cheehowteo https://github.com/cheehowteo any luck?

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/257#issuecomment-1089904975, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALUVOGAB7BUVG4KDTCFV663VDU2RPANCNFSM5PWQ47XQ . You are receiving this because you were mentioned.Message ID: @.***>

--

[image: UM Logo]

Dr. CHEE HOW, TEO Pensyarah Kanan | Senior Lecturer

Pusat Penyelidikan Bioteknologi Pertanian (CEBAR) Centre for Research in Biotechnology for Agriculture Aras 3, Kompleks Pengurusan Penyelidikan & Inovasi Universiti Malaya 50603 Kuala Lumpur, Malaysia Tel: +603-7967 6990/ 6993 | Faks: +603-7967 6991 https://cebar.um.edu.my/

Laboratories: Interactome Laboratory Level 2, High Impact Research (HIR) Building Universiti Malaya 50603 Kuala Lumpur, Malaysia Tel: +603-7967 2701

Genome Informatics Research Laboratory Level 1, High Impact Research (HIR) Building Universiti Malaya 50603 Kuala Lumpur, Malaysia [image: Website] https://www.um.edu.my/ [image: Facebook] https://www.facebook.com/UniversityOfMalaya/ [image: Twitter] https://twitter.com/unimalaya [image: Instagram] https://instagram.com/unimalaya [image: YouTube] https://www.youtube.com/user/UniOfMalaya [image: Tagline]

-- " PENAFIAN: E-mel ini dan apa-apa fail yang dikepilkan bersamanya ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang

termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat-pendapat, rumusan-rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Malaya adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut.

DISCLAIMER: This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of University of Malaya shall be understood as neither given nor endorsed by any of the forementioned. "

oushujun commented 1 year ago

Can you please provide more information on how you installed it? Thanks

Shujun

On Tue, Oct 11, 2022 at 4:57 AM cheehowteo @.***> wrote:

Dear Ou,

I tried to reinstall the EDTA but I still obtained the same error message.

Thank you.

Best regards, Teo

On Wed, Apr 6, 2022 at 3:13 PM Shujun Ou @.***> wrote:

@cheehowteo https://github.com/cheehowteo any luck?

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/257#issuecomment-1089904975, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ALUVOGAB7BUVG4KDTCFV663VDU2RPANCNFSM5PWQ47XQ

. You are receiving this because you were mentioned.Message ID: @.***>

--

[image: UM Logo]

Dr. CHEE HOW, TEO Pensyarah Kanan | Senior Lecturer

Pusat Penyelidikan Bioteknologi Pertanian (CEBAR) Centre for Research in Biotechnology for Agriculture Aras 3, Kompleks Pengurusan Penyelidikan & Inovasi Universiti Malaya 50603 Kuala Lumpur, Malaysia Tel: +603-7967 6990/ 6993 | Faks: +603-7967 6991 https://cebar.um.edu.my/

Laboratories: Interactome Laboratory Level 2, High Impact Research (HIR) Building Universiti Malaya 50603 Kuala Lumpur, Malaysia Tel: +603-7967 2701

Genome Informatics Research Laboratory Level 1, High Impact Research (HIR) Building Universiti Malaya 50603 Kuala Lumpur, Malaysia [image: Website] https://www.um.edu.my/ [image: Facebook] https://www.facebook.com/UniversityOfMalaya/ [image: Twitter] https://twitter.com/unimalaya [image: Instagram] https://instagram.com/unimalaya [image: YouTube] https://www.youtube.com/user/UniOfMalaya [image: Tagline]

-- " PENAFIAN: E-mel ini dan apa-apa fail yang dikepilkan bersamanya ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang

termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat-pendapat, rumusan-rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Malaya adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut.

DISCLAIMER: This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of University of Malaya shall be understood as neither given nor endorsed by any of the forementioned. "

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/257#issuecomment-1274345838, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NFSNSOTPUBIU75OCMDWCUTWBANCNFSM5PWQ47XQ . You are receiving this because you modified the open/close state.Message ID: @.***>