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thread 'main' panicked at 'range start index 3 out of range for slice of length 2', library/core/src/slice/index.rs:52: #31
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Hello, Would you be able to show me what your Cheers, |
Thank you for your help! |
Hi Rhys, I checked the depth file, it seems like the format of my file is wrong. After I feed the correct depth file to rosella, it can run without errors. Thank you very much! Best, |
Hi Rhys, There is a kmer table file in rosella_out/ folder: 58M Jan 19 11:11 rosella_kmer_table.tsv Do you have any idea? Best, |
Hi, Good job figuring out the depth file. Do you have any indication of the quality of the assembly you are trying to provide to rosella is? What is the N50, how many contigs, and what is the overall assembly size in base pairs? Cheers, |
Hi Rhys, I used all the assembly from the MEGAHIT, maybe I need to filter the raw contigs with length (e.g. minimum 1000 bp) first, then feed them to rosella? But I found that rosella has its own filtering for contig length (1500 bp). contigs (>= 0 bp) 22503179 Thanks for all your help. Li Zhao |
Hi Li, I'm unsure what would be causing this issue. I'll have to take a closer look, would you be able to send me through the coverage file and the assembly and I'll see if I can get a more informative error to be produced? Cheers, |
Hi Rhys, Just in case, I also paste it here: Thanks for all your help. Best, Li |
Hi Li, Sorry have just gotten around to this properly. These files are really big, I'm wondering if your machine is running out memory trying to process them? How much RAM does your machine have? cheers, |
Hi Rhys, Best, Li |
Hi Li, Would you be able to check something for me?
replacing the kmer table with the one previously produced and the output folder with the previous one as well? And then post what the error says? I think there might be a strange dependency issue occuring with skbio Cheers, |
I'm hoping this is fixed in |
Hi there,
I run rosella with command "rosella recover -i group-MetaGeno_mb2_depth.txt -r MEGAHIT-group-MetaGeno.contigs.fa --output-directory ./rosella_out/ --threads 14"
But after it build the index, I got an error like:
thread 'main' panicked at 'range start index 3 out of range for slice of length 2', library/core/src/slice/index.rs:52:
note: run with
RUST_BACKTRACE=1
environment variable to display a backtraceAnd it stoped.
Could you help me to check, what's the problem?
Thank you!
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