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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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Empty Output (non-memory-related issue) #236

Closed lidi4 closed 1 year ago

lidi4 commented 1 year ago

Hello,

I've been trying to run Racon for the first time on one ONT dataset (here)

Each time I try to run it, with or without the specified options, it runs very quickly with no errors and spits out an empty file. What is happening here? Any help would be so appreciated!!

My command: racon -m 8 -x -6 -g -8 SRR12390956.fastq aln-se.sam assembly.fasta > polished1_assembly.fasta

Log: [racon::Polisher::initialize] loaded target sequences 0.001896 s [racon::Polisher::initialize] loaded sequences 0.364408 s [racon::Polisher::initialize] loaded overlaps 0.328071 s [racon::Polisher::initialize] aligning overlaps [====================] 0.563149 s [racon::Polisher::initialize] transformed data into windows 0.046840 s [racon::Polisher::polish] generating consensus [====================] 0.002845 s [racon::Polisher::] total = 1.317226 s

Racon is being operated in its own conda env.

Data on the read input file: number of sequences: 7911 number of base pairs: 54 Mbp Read file size: 2.2G

Assembly file generate with Flye (metaFlye) SAM file generated with BWA

according to metaQUAST assembly QC, the assembly file has 25 contigs ( if that's helpful, idk) all three input files are valid and full, no corruption.

Not sure how/why, but when I check racon version it says 1.5.0 despite that appearing to be too high of a version? I can't explain that

rvaser commented 1 year ago

Hello, The fastq file you are using has all qualities set to $ which is QV3, while racon has:

    -q, --quality-threshold <float>
        default: 10.0
        threshold for average base quality of windows used in POA

which means all reads are filtered out and no polishing is done.

Regarding v1.5.0, racon development has been transfered to lbcb-sci/racon repository some time ago.

Best regards, Robert

rvaser commented 1 year ago

If this does not resolve your issue, please reopen.

lidi4 commented 1 year ago

Thank you so much!! I will let you know if anything else pops up asap.

On Fri, May 12, 2023, 1:41 PM Robert Vaser @.***> wrote:

Hello, The fastq file you are using has all qualities set to $ which is QV3, while racon has:

-q, --quality-threshold <float>
    default: 10.0
    threshold for average base quality of windows used in POA

which means all reads are filtered out and no polishing is done.

Regarding v1.5.0, racon development has been transfered to lbcb-sci/racon repository some while ago.

Best regards, Robert

— Reply to this email directly, view it on GitHub https://github.com/isovic/racon/issues/236#issuecomment-1546076377, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6ZWZXVBMTHKCGTTW7MQITLXFZY4ZANCNFSM6AAAAAAX2JDDYI . You are receiving this because you authored the thread.Message ID: @.***>