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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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SMARTdenovo failure #23

Closed gabster closed 6 years ago

gabster commented 6 years ago

Hi, I run SMARTdenovo on some canu corrected reads. In the end it finished with this error message: CA690_canu.mak:27: recipe for target 'CA690_canu.dmo.cns' failed make: *** [CA690_canu.dmo.cns] Error 1

What can I do? Cheers Gabi

ruanjue commented 6 years ago

Please check the file CA690_canu.dmo.lay, whether it exists?

gabster commented 6 years ago

Yes, it does exist

ruanjue commented 6 years ago

Can you have a look at CA690_canu.dmo.cns.log, and give me more message.

gabster commented 6 years ago

Dear Jue, I am attaching the log file. Thanks Gabi

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Jue Ruan [mailto:notifications@github.com] Gesendet: Donnerstag, 30. August 2018 13:28 An: ruanjue/smartdenovo Cc: Margos, Gabriele, Dr. (LGL); Author Betreff: Re: [ruanjue/smartdenovo] SMARTdenovo failure (#23)

Can you have a look at CA690_canu.dmo.cns.log, and give me more message.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ruanjue/smartdenovo/issues/23#issuecomment-417286278, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aoo3YUQJ92OeyeSCF55RVYrIyku-9WHlks5uV8xcgaJpZM4WPv7O.

ruanjue commented 6 years ago

I cannot find the log file.

gabster commented 6 years ago

Hi, it was attached to the mail. I am copying it here:

[Tue Aug 28 18:25:09 2018]"utg4 length=182973 nodes=239" init [Tue Aug 28 18:25:09 2018]"utg4 length=182973 nodes=239" generate backbone length=183036 [Tue Aug 28 18:25:11 2018]"utg4 length=182973 nodes=239" align aln_score=3130893 [Tue Aug 28 18:25:11 2018]"utg4 length=182973 nodes=239" merge nodes [Tue Aug 28 18:25:11 2018]"utg4 length=182973 nodes=239" iter1 length=187454 aln_score=3130893 cns_score=813878.312500 [Tue Aug 28 18:25:12 2018]"utg4 length=182973 nodes=239" align aln_score=3302350 [Tue Aug 28 18:25:12 2018]"utg4 length=182973 nodes=239" merge nodes [Tue Aug 28 18:25:12 2018]"utg4 length=182973 nodes=239" iter2 length=187054 aln_score=3302350 cns_score=806780.625000 [Tue Aug 28 18:25:14 2018]"utg4 length=182973 nodes=239" align aln_score=3307951 [Tue Aug 28 18:25:14 2018]"utg4 length=182973 nodes=239" merge nodes [Tue Aug 28 18:25:14 2018]"utg4 length=182973 nodes=239" iter3 length=187167 aln_score=3307951 cns_score=807200.500000 [Tue Aug 28 18:25:15 2018]"utg4 length=182973 nodes=239" align aln_score=3308283 [Tue Aug 28 18:25:15 2018]"utg4 length=182973 nodes=239" merge nodes [Tue Aug 28 18:25:15 2018]"utg4 length=182973 nodes=239" iter4 length=187059 aln_score=3308283 cns_score=806998.125000 [Tue Aug 28 18:25:16 2018]"utg4 length=182973 nodes=239" align aln_score=3308078 [Tue Aug 28 18:25:16 2018]"utg4 length=182973 nodes=239" merge nodes [Tue Aug 28 18:25:16 2018]"utg4 length=182973 nodes=239" iter5 length=187167 aln_score=3308078 cns_score=807204.312500 [Tue Aug 28 18:25:18 2018]"utg4 length=182973 nodes=239" align aln_score=3308268 [Tue Aug 28 18:25:18 2018]"utg4 length=182973 nodes=239" merge nodes [Tue Aug 28 18:25:18 2018]"utg4 length=182973 nodes=239" iter6 length=187053 aln_score=3308268 cns_score=806977.562500 [Tue Aug 28 18:25:18 2018]"utg5 length=889920 nodes=10067" init [Tue Aug 28 18:25:18 2018]"utg5 length=889920 nodes=10067" generate backbone length=889991 -- Out of memory, try to allocate 3489660915 bytes, old size 1610612730, old addr 0x7f66f37e4010 in encap_list -- list.h:65 --

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Margos, Gabriele, Dr. (LGL) Gesendet: Donnerstag, 30. August 2018 13:53 An: 'ruanjue/smartdenovo'; ruanjue/smartdenovo Cc: Author Betreff: AW: [ruanjue/smartdenovo] SMARTdenovo failure (#23)

Dear Jue, I am attaching the log file. Thanks Gabi

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Jue Ruan [mailto:notifications@github.com] Gesendet: Donnerstag, 30. August 2018 13:28 An: ruanjue/smartdenovo Cc: Margos, Gabriele, Dr. (LGL); Author Betreff: Re: [ruanjue/smartdenovo] SMARTdenovo failure (#23)

Can you have a look at CA690_canu.dmo.cns.log, and give me more message.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ruanjue/smartdenovo/issues/23#issuecomment-417286278, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aoo3YUQJ92OeyeSCF55RVYrIyku-9WHlks5uV8xcgaJpZM4WPv7O.

ruanjue commented 6 years ago

-- Out of memory, try to allocate 3489660915 bytes, old size 1610612730, old addr 0x7f66f37e4010 in encap_list -- list.h:65 -- Out of memory! Please find a PC with larger RAM.

gabster commented 6 years ago

Hi Jue, I am sorry, I did not see that. I had a previous run on same data without canu correction and that worked. Thanks for your support, Gabi

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Jue Ruan [mailto:notifications@github.com] Gesendet: Donnerstag, 30. August 2018 14:17 An: ruanjue/smartdenovo Cc: Margos, Gabriele, Dr. (LGL); Author Betreff: Re: [ruanjue/smartdenovo] SMARTdenovo failure (#23)

-- Out of memory, try to allocate 3489660915 bytes, old size 1610612730, old addr 0x7f66f37e4010 in encap_list -- list.h:65 -- Out of memory! Please find a PC with larger RAM.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ruanjue/smartdenovo/issues/23#issuecomment-417298334, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aoo3Yb2nnlnza4U7mThe2MQH-zxKV689ks5uV9eggaJpZM4WPv7O.