Can't submit metaSPAdes_assemble script using ${PBS_ARRAYID} when having the my_data_set.yaml file? #983
Replies: 5 comments
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Sorry, I do not follow what the problem is. Maybe you'd just generate YAML from your PBS script? |
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Thank you very much for replying me. My question is that I can't directly run the command line with ${PBS_ARRAYID} as below due to I am using the "my_data_set.yaml" dataset file. The command line with ${PBS_ARRAYID} The command line with "my_data_set.yaml" dataset file, which I am running now. Best, Bing |
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Well, exactly as I said: you'd need to generate YAML file from your PBS script. And use it for SPAdes run. Hope it helps |
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Thank you very much for your quick response. I need to generate one YAML file for each of my paired-end file like below? When I submit my PBS shell script on HPC, can I submit with 6 inconsistent job ids - "PBS -t 25,27,29,31-36%3"? Then, I can submit 3 jobs at the same time? |
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No. You need to generate the contents of this file as necessary
No idea. You may want to ask your system administrator about this. |
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Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above.
Dear metaSPAdes support team,
I am now assembling 9 paired-end samples using command line below. But, as my sample id is inconsistent, eg., 25,27, 29, 31-36. So, I use the .yaml file as the input of --dataset. But, if I write the absolute path of paired-end .fq.gz files, then I can't use the array id in my PBS job setting. For example, I can specify setting like, PBS -t 25,27,29,31-36%3 or ${PBS_ARRAYID}.
Could you give some suggestions on my question?
Command line
/services/tools/SPAdes/3.15.3/bin/spades.py --meta -k 21,33,55,77 --dataset /PATH_TO_YAML_FILE/my_data_set.yaml -t 40 -m 1500 -o /PATH_TO_OUPUT/spades_output_25_36
--dataset - my_data_set.yaml.txt
my_data_set copy.yaml.txt
Best,
Bing
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