Thanks a lot! Your video is very helpful and easy to follow! I'm at the final stage of assembly the reads. But I got this message: [2023-04-07 21:51:42] INFO: Starting Flye 2.9.2-b1786 [2023-04-07 21:51:42] INFO: >>>STAGE: configure [2023-04-07 21:51:42] INFO: Configuring run [2023-04-07 21:51:45] INFO: Total read length: 107266283 [2023-04-07 21:51:45] INFO: Input genome size: 5600000 [2023-04-07 21:51:45] INFO: Estimated coverage: 19 [2023-04-07 21:51:45] INFO: Reads N50/N90: 1120 / 426 [2023-04-07 21:51:45] INFO: Minimum overlap set to 1000 [2023-04-07 21:51:45] INFO: >>>STAGE: assembly [2023-04-07 21:51:45] INFO: Assembling disjointigs [2023-04-07 21:51:45] INFO: Reading sequences [2023-04-07 21:51:47] ERROR: Caught unhandled exception: std::bad_alloc [2023-04-07 21:51:47] ERROR: flye-modules(+0x40193) [0x56435fd5a193] [2023-04-07 21:51:47] ERROR: /home/genome/anaconda3/envs/genome_assembly/bin/../lib/libstdc++.so.6(+0xb0514) [0x7fe8cb35d514] [2023-04-07 21:51:47] ERROR: /home/genome/anaconda3/envs/genome_assembly/bin/../lib/libstdc++.so.6(+0xb0566) [0x7fe8cb35d566] [2023-04-07 21:51:47] ERROR: /home/genome/anaconda3/envs/genome_assembly/bin/../lib/libstdc++.so.6(__cxa_rethrow+0) [0x7fe8cb35d758] [2023-04-07 21:51:47] ERROR: /home/genome/anaconda3/envs/genome_assembly/bin/../lib/libstdc++.so.6(_Znwm+0x59) [0x7fe8cb35db85] [2023-04-07 21:51:47] ERROR: flye-modules(+0x70585) [0x56435fd8a585] [2023-04-07 21:51:47] ERROR: flye-modules(+0x3ce90) [0x56435fd56e90] [2023-04-07 21:51:47] ERROR: flye-modules(+0x18872) [0x56435fd32872] [2023-04-07 21:51:47] ERROR: /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7fe8cafa3d90] [2023-04-07 21:51:47] ERROR: /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7fe8cafa3e40] [2023-04-07 21:51:48] ERROR: Command '['flye-modules', 'assemble', '--reads', '/home/genome/nanoporeR1_trimmed.fa', '--out-asm', '/home/genome/assembly/00-assembly/draft_assembly.fasta', '--config', '/home/genome/anaconda3/envs/genome_assembly/lib/python3.10/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg', '--log', '/home/genome/assembly/flye.log', '--threads', '10', '--genome-size', '5600000', '--min-ovlp', '1000']' died with . [2023-04-07 21:51:48] ERROR: Pipeline aborted What should I do? this is my first time ever doing coding 😆
@bioinformaticscoach
Жыл бұрын
I suggest you report this issue. Here is the developer's page: github.com/fenderglass/Flye/issues
@aymsagagi
3 ай бұрын
That is a great tutorial. We thank you for that! My question is, i have my sequence file stored in windows, instead of importing data from internet using "wget + url" how can i import my own data? Also, how can i export the output since i have my linux installed in windows using ubuntu... Many questions :). Thank you in advance!!
@lazizasamov440
5 ай бұрын
God bless you man great content!
@forbesavila8006
2 жыл бұрын
How do you check if the contigs are complete contigs? Thank you for all the videos it helps me a lot!
@henrikalmblad7450
Жыл бұрын
Great tutorial! Thank you for sharing.
@diyap7343
2 жыл бұрын
This channel is such a gold mine for bioinformatics! I had a question about this assembly though. I have about 900 long read fastq files belonging to a bacteria. Should I be running this command individually for each fastq file? Also can I use a fastq file as input for flye? or does it have to be fasta only?
@bioinformaticscoach
2 жыл бұрын
Thanks for the message. In such a situation you have to create a loop. I am planning on making a video on that. First I need to get some datasets. I am currently searching for free datasets online. Once I do that I will make the video.
@bioinformaticscoach
2 жыл бұрын
If the data is publicly available, you can send me the link. I will look at the data .
@user-bz2or9pd8z
2 жыл бұрын
great tutorial
@bioinformaticscoach
2 жыл бұрын
Thanks!
@muhammadnafees6192
11 ай бұрын
Great Video, How to assemble draft genome? thanks
@alloycore4965
2 жыл бұрын
Thank you very much! It is quite helpful :)
@silmiyusrirahmadani19
Жыл бұрын
the command is not found after i make add channels bioconda what matters?
@xuhangwu1770
9 ай бұрын
silly question, about the threads. how do you decide how many threads?
@SimonBoafo
2 ай бұрын
check your core processor to determine that if not you can just paste your exact pc brand and model online and it will pop up
@kennedychibesa9809
Жыл бұрын
Hi. How do I perform multiple assemblies from different samples?
@bioinformaticscoach
Жыл бұрын
You need to write a bash script for that or use workflow managers like nextflow, snakemake, etc. You can also book a session and we will try to work it out.
2 жыл бұрын
Hi, good morning! thank you so much for the video! I have a question! please could do you help me? When we have the assembly of our genome sequence, How can we organize these assemblies in already organized chromosomes? For example, I have a reference genome, which is organized in 35 chromosomes, how could I manage to organize my genome in different chromosomes? Thanks!
@bioinformaticscoach
2 жыл бұрын
I don't get the question. Please come again.
2 жыл бұрын
@@bioinformaticscoach Hi, good morning! thank you so much for the video! I have a question! please could do you help me? When we have the assembly of our genome sequence, How can we organize these assemblage in already organized chromosomes? For example, I have a reference genome, which is organized in 35 chromosoms, how could I manage to organize my genome in different chromosoms? Thanks!
@Tech-nh2pg
2 жыл бұрын
Hi. How can I do assemble with medaka after I done with Flye?
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