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Published 20 hours ago • verified publisher icon oushujun

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

Open cheehowteo opened this issue 2 years ago • 2 comments

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_RM_TE.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

cheehowteo avatar Mar 02 '22 07:03 cheehowteo

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_RM_TE.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

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oushujun avatar Mar 02 '22 14:03 oushujun

@cheehowteo any luck?

oushujun avatar Apr 06 '22 07:04 oushujun

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?

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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.

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cheehowteo avatar Oct 11 '22 08:10 cheehowteo

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?

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. 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.

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oushujun avatar Oct 18 '22 03:10 oushujun