thread 'main' panicked at 'range start index 3 out of range for slice of length 2', library/core/src/slice/index.rs:52:

[Jolvii85]

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 backtrace
And it stoped.

Could you help me to check, what's the problem?

Thank you!

[rhysnewell]

Hello,

Would you be able to show me what your group-MetaGeno_mb2_depth.txt file looks like?

Cheers,
Rhys

[Jolvii85]

Hello,

Would you be able to show me what your group-MetaGeno_mb2_depth.txt file looks like?

Cheers, Rhys
Hi Rhys,
The depth file looks like this:
k141_7783846 23.7211
k141_4245736 7.71226
k141_21228664 2.38346
k141_19813420 3.75191
k141_15567689 12

Thank you for your help!

[Jolvii85]

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,

[Jolvii85]

Hi Rhys,
Now, there are new errors:
[2023-01-19T09:43:38Z INFO rosella] rosella version 0.4.2
[2023-01-19T09:43:38Z INFO rosella] Using min-covered-fraction 0%
[2023-01-19T09:43:38Z INFO rosella] Using min-read-aligned-percent 0%
[2023-01-19T10:13:27Z ERROR bird_tool_utils::command] Error when running flight process. Exitstatus was : ExitStatus(unix_wait_status(256))
thread 'main' panicked at 'Failed to grab stderr from failed flight process', /home/conda/.cargo/registry/src/github.com-1ecc6299db9ec823/bird_tool_utils-0.3.0/src/command.rs:17:14
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

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,

[rhysnewell]

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,
Rhys

[Jolvii85]

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
contigs (>= 1000 bp) 3277097
contigs (>= 5000 bp) 263856
contigs (>= 10000 bp) 86370
contigs (>= 25000 bp) 19635
contigs (>= 50000 bp) 5314
Total length (>= 0 bp) 17640040897
Total length (>= 1000 bp) 8556999382
Total length (>= 5000 bp) 3101574521
Total length (>= 10000 bp) 1903096983
Total length (>= 25000 bp) 918924844
Total length (>= 50000 bp) 434733433
contigs 10296633
Largest contig 713443
Total length 13288242988
GC (%) 47.28
N50 1527
N75 781
L50 1701970
L75 4882146
N's per 100 kbp 0.00
predicted rRNA genes 1421 + 572 part

Thanks for all your help.

Li Zhao

[rhysnewell]

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,
Rhys

[Jolvii85]

Hi Rhys,
The size of the files is big. I have sent the link to your Gmail.

Just in case, I also paste it here:
https://drive.google.com/file/d/1vOnQuDqnRaxasqMGPXInzpXjhrfxfTBo/view?usp=share_link
https://drive.google.com/file/d/1XymHT6NbNJAveejda7RUbl9etC5BFgqR/view?usp=share_link

Thanks for all your help.

Best,

Li

[rhysnewell]

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,
Rhys

[Jolvii85]

Hi Rhys,
The node I used has 3.72T RAM, so it should not be a memory error.

Best,

Li

[rhysnewell]

Hi Li,

Would you be able to check something for me?
Could you run flight by itself? i.e.

flight bin --input MEGAHIT-group-MetaGeno-depth.txt --kmer_frequencies rosella_test/rosella_kmer_table.tsv --assembly MEGAHIT-group-MetaGeno.contigs.fa --cores 8 --output_directory rosella_test/

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,
Rhys

[rhysnewell]

I'm hoping this is fixed in v0.5.0, error should at least be exposed. Please create a new issue with the error from flight if you still experience this