## How to continue the uncompleted tasks?

[laiqiang0728]

Hi,

I'm running a task to assmemble thousands of genes, and it has token about a week. But our servers is offline due to a sudden and irresistible event, so my task was interrupted, and the previous task have completed 70%. I really want to know if aTRAM has any command that can continue the unfinshed task, otherwise I would cost much more time to start all over again.

Looking forward to your kindly reply.

[juliema]

totally agree. We have a script that can determine how far your job went and set up a new job. This is unofficial so it is not live yet. Will send soon.

On Tue, Jul 5, 2022 at 7:03 AM laiqiang0728 @.***> wrote:

Hi,

I'm running a task to assmemble thousands genes, and it has token about a week. But our servers is offline due to a sudden and irresistible event, so my task was interrupted, and the previous task have completed 70%. I really want to know if aTRAM has any command that can continue the unfinshed task, otherwise I would cost much more time to start all over again.

Looking forward to your kindly reply.

— Reply to this email directly, view it on GitHub https://github.com/juliema/aTRAM/issues/315, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA2AZ3RDMLHYD3WC5UA6STTVSQ6DTANCNFSM52WKZOGA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[danielyao12]

Hi @laiqiang0728,

I try to use the aTRAM to assemble orhologs, but I got error that

ERROR: Exception: [Errno 2] No such file or directory: /data/backbone_tree/dqgg_analysis/atram_analysis/dqgg0001_temp/atram_ngyw_1fc/DQGG0001_3380ogs_polyneura_header_ILEX2_2.fasta_01_w3hepd6w/output.fasta-unitigs.fa'

The command I used was : /data/software/aTRAM/atram.py --cpus 10 -p \\ --temp-dir=/data/backbone_tree/dqgg_analysis/atram_analysis/dqgg0001_temp --keep-temp-dir \\ --path=~/anaconda3/envs/atram-env/bin \\ --blast-db=dqgg0001_output/DQGG0001 \\ -Q=3380ogs_polyneura_header.fa \\ --assembler=abyss \\ --output-prefix=dqgg0001_output/DQGG0001_atram. Could you please show me the command you used? Thank you very much for your time!

[laiqiang0728]

Hi，@danielyao12

I had a similar ERROR once, I used the Trinity as the assembly tools, so the ERROR noted that “Exception: [Errno 2] No such file or directory: /path..../***.trinity.fasta”. I eventually found the problem was that the Trinity had not been installed correctly. So may be your ERROR also caused by the assembly tools.

And the command I used was : /path/atram.py -b=/path/atram_db/prefix -Q=/path/querysequences(.fasta) -o=/outpath --assembler=trinity -T 1200 --log-file /path/.atram.log --log-level info

Hope it's helpful for you!

[laiqiang0728]

totally agree. We have a script that can determine how far your job went and set up a new job. This is unofficial so it is not live yet. Will send soon. … On Tue, Jul 5, 2022 at 7:03 AM laiqiang0728 @.> wrote: Hi, I'm running a task to assmemble thousands genes, and it has token about a week. But our servers is offline due to a sudden and irresistible event, so my task was interrupted, and the previous task have completed 70%. I really want to know if aTRAM has any command that can continue the unfinshed task, otherwise I would cost much more time to start all over again. Looking forward to your kindly reply. — Reply to this email directly, view it on GitHub <#315>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA2AZ3RDMLHYD3WC5UA6STTVSQ6DTANCNFSM52WKZOGA . You are receiving this because you are subscribed to this thread.Message ID: @.>

Thanks for your quick reply, and I'm looking forward to the new script.

[juliema]

Here is a script that will detereine which loci were not assembled and will build a new query file with the remaining loci to assemble so you can just start the run with that new query file.

You need your original query file and a list of all the assembled files.

For example:

ls filtered_contigs >list.txt

the only thing to watch out is if your original locus names have dots they might have been converted to underscores by atram output.

Then you can run this script with: python3 new_target_file.py

It will ask you for the info it needs.

Thanks!

From: Julie Allen @.> Date: Wednesday, July 6, 2022 at 4:47 PM To: juliema/aTRAM @.>, Julie Allen @.> Cc: juliema/aTRAM @.>, Subscribed @.***> Subject: Re: [juliema/aTRAM] ## How to continue the uncompleted tasks? (Issue #315) totally agree. We have a script that can determine how far your job went and set up a new job. This is unofficial so it is not live yet. Will send soon.

On Tue, Jul 5, 2022 at 7:03 AM laiqiang0728 @.**@.>> wrote:

Hi,

I'm running a task to assmemble thousands genes, and it has token about a week. But our servers is offline due to a sudden and irresistible event, so my task was interrupted, and the previous task have completed 70%. I really want to know if aTRAM has any command that can continue the unfinshed task, otherwise I would cost much more time to start all over again.

Looking forward to your kindly reply.

— Reply to this email directly, view it on GitHubhttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjuliema%2FaTRAM%2Fissues%2F315&data=05%7C01%7Cjallen23%40unr.edu%7C2466e7a088d943bf733d08da5f90cd4e%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C0%7C0%7C637927372769712097%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=EfAFTqdfKWweAFT5inOETYzEAKebeeIRj1J7eKoYV%2FQ%3D&reserved=0, or unsubscribehttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAA2AZ3RDMLHYD3WC5UA6STTVSQ6DTANCNFSM52WKZOGA&data=05%7C01%7Cjallen23%40unr.edu%7C2466e7a088d943bf733d08da5f90cd4e%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C0%7C0%7C637927372769712097%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lIKuzhCONJFqrpzG%2BlqerUb2h4UfmP272Yq1hOfY1PI%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>