Problem in bin refinement step #14
Comments
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Hello, It seems that no candidate bins were successfully generated using MaxBin2, as they were either too small (<50 Kb) or too large (>20 Mb). This is why the bin refinement step exited. If you had sufficient sequencing coverage, my best guess is that the metagenome has very low microbial diversity. Here is my suggestion: you can try bin refinement using MetaBAT2 and SemiBin with the following command: If it works, you can ignore the previous error and re-run the same command. If it does not work, try checking the input long reads (accuray/length/etc). Best |
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Hi, Best |
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It seems that there are some errors in the taxonomy inference with GTDB-Tk. Could you please provide the log file for the GTDB-Tk step? It should be located in the folder |
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Hi, Thank you for the code.. |
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Now I understand what happened. It seems that the GTDB database was not set up for GTDB-Tk. You can refer to this section for instructions on how to set it up. Let me know if it doesn't work after the database setup:) |
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HI, Well I downloaded both the databases and everything was set up according to your referred section. I ran the code again. It went well initially but at the end error came due to fastani. I looked into the folder where gtdbtk was extracted i.e, "release220". Strangely I saw no folder called fastani.. What could go wrong.. I have properly downloaded and extracted the databases. Although I had to use different web url to download it as it has changed.
The error is given below.. |
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Hi, it might be my mistake. The last time I updated nanophase, I upgraded the GTDB database from R207 to R214. However, the latest version available today is R220, which has a different structure. Unfortunately, if you want to use the current version of nanophase, you will need to download R214 and configure the path accordingly. I apologize for the inconvenience. the commands that you may refer to: |
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Yes, Thanks a ton for it. I am running the code and it is downloading. I will surely update you after running the codes. Can you help me by understanding one thing. Nanophase is very good for ONT fastq reads. But I also have many shotgun metagenome sequenced (2x250bp) samples. I have done assembly binning using IDBA-UD and MEGAHIT. Can those assembled contigs be used in any stage of this Nanophase pipeline. I actually similarly wanted to perform MAG based analysis from shotgun metagenome data. But not finding any comprehensive single pipeline for that. Nanophase is really a comprehensive pipeline for ONT fastqs. Can you help me on this? |
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No problem:) If the shotgun metagenome reads come from the same sample as the long reads, you can use nanophase with the If you already have MAGs, they can technically be used in the nanophase pipeline, but I wouldn't suggest that approach. Instead, I recommend processing them separately: you can run CheckM/CheckM2 for quality assessment, GTDB-Tk for taxonomic assignment and phylogenetic tree construction, DRAM/Bakta for quick genome annotations, CoverM/sylph for abundance estimation and etc. |
I am using Metagenomic data. I have a 120 core server system.
Please see the error below. I have encountered problem in bin refinement step.
In the log file it is saying
"Skipping nanophase-out/02-LongBins/INITIAL_BINNING/metabat2/metabat2-bins//bin.22.fa because the bin size is not between 50kb and 20Mb"
or
"Skipping nanophase-out/02-LongBins/INITIAL_BINNING/maxbin2/maxbin2-bins//bin.001.fasta because the bin size is not between 50kb and 20Mb"
and then
"there are 0 bins in binsB"
"Please provide valid input. Exiting..."
I have also added the bin_refinement.log file here..
bin_refinement.log
Please help
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