search

lmlui / Jorg

MAG Circularization Method
GNU General Public License v3.0
33 stars 5 forks source link

Error running tool #10

Closed mdsufz closed 1 year ago

mdsufz commented 2 years ago

Hi, I really am interested in getting this tool to work on my data. However, I am getting a weird error that I haven't been able to fix.

Here is the mirabait_iteration_1.log file

Baiting sequences with at least 1 exact kmer matches. Creating directory ./mirakmc_a563-95aa-10c5-3094 ... done. Localtime: Thu Sep 22 11:30:06 2022 hashstat_t: 24 freemem: 377414430720 Percentage mbfb1: 269947 mbfb2: 269947 HS_nepb: 737135274 Std exception caught. Message: std::bad_alloc Deleting directory ./mirakmc_a563-95aa-10c5-3094 ... done.

Also here is the manifest.conf file (it seems to be ok).

project = UNDR01_190A18-bin.3 job = genome,denovo,accurate parameters = -NW:cac=warn -CO:fnic=yes -AS:nop=6:sdlpo=no -KS:fenn=0.3 -OUT:rtd=yes

readgroup = UNDR01_190A18-bin.3 data = UNDR01_190A18-bin.3_1.fastq UNDR01_190A18-bin.3_2.fastq technology = solexa autopairing

And lastly, here is the log file when running the code (jorg -b UNDR01_190A18-bin.3.fa -r interleaved_UNDR01_190A18-bin.3.fastq -k 33 -c 5 -i 5 --high_contig_num no):

Jorg run on Thu Sep 22 11:30:06 CEST 2022

User environment details: MIRA path: /software/easybuild-broadwell/software/MIRA/5.0rc2-foss-2020b/bin/mira MIRA version: V5rc2 MIRABAIT path: /software/easybuild-broadwell/software/MIRA/5.0rc2-foss-2020b/bin/mirabait MIRABAIT version: V5rc2 seqtk path: /software/easybuild-broadwell/software/seqtk/1.3-GCC-10.2.0/bin/seqtk

Start running Jorg Start: make manifest file for MIRA End: make manifest file for MIRA Start: generating new directory named 'Iterations' End: generating new directory named 'Iterations'

Start: Jorg iteration # 1 Start: recruiting reads with mirabait

Any idea why it is not working?

Best regards, Joao

(at this point it stops)

lmlui commented 2 years ago

Hi Joao,

There's an error that happens when the fasta file with the bin and the fastq file with the reads have the same name. I think that Jorg isn't catching it because you have a period in the file prefixes (the period before the '3' in the names). Try changing the file names so that they are different and there are no periods in the file prefixes before the file extensions. Let me know if that doesn't work.

Best,

Lauren

mdsufz commented 2 years ago

Hi Lauren,

Thanks for your reply. I did as you suggest but I still receive the same error.

I changed the names of the files eliminating the periods before the extensions:

UNDR01_190A18_bin_3.fa interleaved_UNDR01_190A18_bin_3.fastq

Any other suggestions?

Best regards, Joao

mdsufz commented 2 years ago

Hi Lauren,

So a quick update. Since I was submitting this job to a HPC I was unsure what the potential problems from our side would be. I now have managed to get this running on our cluster. Basically, the memory specification was missing.

Thanks for the help.

Cheers, Joao

lmlui commented 2 years ago

Dear Joao,

Okay, great! I'm glad that you were able to figure it out.

Best,

Lauren

mdsufz commented 2 years ago

Hi Lauren,

So I received another error.

[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] Seen signal: 7

Aborting process due to an external cause. Please check the lines above in this ouput for more information.

Any ideas?

Best regards, Joao

tnn111 commented 2 years ago

Joao,

This is probably exactly what it says. Somehow a CTRL-C was sent. It’s not a MIRA error or a script error. Any chance you hit it on the keyboard?

Thanks, Torben

On Sep 26, 2022, at 00:19, mdsufz @.***> wrote:

Hi Lauren,

So I received another error.

[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] Seen signal: 7

Wrapped MIRA process was terminated by a signal. CTRL-C may have been a cause. MIRA stopped due to an external signal * ->Thrown: void miraMain_launchWrapped(int argc, char ** argv) ->Caught: main

Aborting process due to an external cause. Please check the lines above in this ouput for more information.

Any ideas?

Best regards, Joao

— Reply to this email directly, view it on GitHub https://github.com/lmlui/Jorg/issues/10#issuecomment-1257585715, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMXPRXAIXF3BK7OEO4KH33WAFE6TANCNFSM6AAAAAAQS5XG64. You are receiving this because you are subscribed to this thread.

mdsufz commented 2 years ago

Hi Torben,

I do not remember cancelling the job.

I will try again and make sure CTRL+C is not pressed.

Best regards, Joao

On 26/09/22 20:56, Torben Nielsen @.***> wrote:

Joao,

This is probably exactly what it says. Somehow a CTRL-C was sent. It’s not a MIRA error or a script error. Any chance you hit it on the keyboard?

Thanks, Torben

On Sep 26, 2022, at 00:19, mdsufz @.***> wrote:

Hi Lauren,

So I received another error.

[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] Seen signal: 7

Wrapped MIRA process was terminated by a signal. CTRL-C may have been a cause. MIRA stopped due to an external signal * ->Thrown: void miraMain_launchWrapped(int argc, char ** argv) ->Caught: main

Aborting process due to an external cause. Please check the lines above in this ouput for more information.

Any ideas?

Best regards, Joao

— Reply to this email directly, view it on GitHub https://github.com/lmlui/Jorg/issues/10#issuecomment-1257585715, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMXPRXAIXF3BK7OEO4KH33WAFE6TANCNFSM6AAAAAAQS5XG64. You are receiving this because you are subscribed to this thread.

— Reply to this email directly, view it on GitHub(https://github.com/lmlui/Jorg/issues/10#issuecomment-1258471119 ), or unsubscribe(https://github.com/notifications/unsubscribe-auth/AMXWJGMEFBTXR42HYURYI3DWAHWWRANCNFSM6AAAAAAQS5XG64 ). You are receiving this because you modified the open/close state.Message ID: @.***>

--

Best regards,

Joao Saraiva

Department of Environmental Microbiology Group of Microbial Systems Bioinformatics Helmholtz Centre for Environmental Research - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone: +49 341 235 - 1374 Email: @.*** WWW: http://www.ufz.de

tnn111 commented 2 years ago

Hi Joao,

Is it possible that a systems admin sent the signal because of resource use? I don’t know what else to tell you. Other than maybe to try it with a subset of the data to see if the problem is dependent on the amount of data you have.

Thanks, Torben

On Sep 28, 2022, at 00:28, mdsufz @.***> wrote:

Hi Torben,

I do not remember cancelling the job.

I will try again and make sure CTRL+C is not pressed.

Best regards, Joao

On 26/09/22 20:56, Torben Nielsen @.***> wrote:

Joao,

This is probably exactly what it says. Somehow a CTRL-C was sent. It’s not a MIRA error or a script error. Any chance you hit it on the keyboard?

Thanks, Torben

On Sep 26, 2022, at 00:19, mdsufz @.***> wrote:

Hi Lauren,

So I received another error.

[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] Seen signal: 7

Wrapped MIRA process was terminated by a signal. CTRL-C may have been a cause. MIRA stopped due to an external signal * ->Thrown: void miraMain_launchWrapped(int argc, char ** argv) ->Caught: main

Aborting process due to an external cause. Please check the lines above in this ouput for more information.

Any ideas?

Best regards, Joao

— Reply to this email directly, view it on GitHub https://github.com/lmlui/Jorg/issues/10#issuecomment-1257585715, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMXPRXAIXF3BK7OEO4KH33WAFE6TANCNFSM6AAAAAAQS5XG64. You are receiving this because you are subscribed to this thread.

— Reply to this email directly, view it on GitHub(https://github.com/lmlui/Jorg/issues/10#issuecomment-1258471119 ), or unsubscribe(https://github.com/notifications/unsubscribe-auth/AMXWJGMEFBTXR42HYURYI3DWAHWWRANCNFSM6AAAAAAQS5XG64 ). You are receiving this because you modified the open/close state.Message ID: @.***>

--

Best regards,

Joao Saraiva

Department of Environmental Microbiology Group of Microbial Systems Bioinformatics Helmholtz Centre for Environmental Research - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone: +49 341 235 - 1374 Email: @.*** WWW: http://www.ufz.de — Reply to this email directly, view it on GitHub https://github.com/lmlui/Jorg/issues/10#issuecomment-1260499127, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMXPRWNY4UTINRA4MV6OATWAPXSHANCNFSM6AAAAAAQS5XG64. You are receiving this because you commented.