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failed to get modbase info for record ..., Skipped: AUX data not found #159
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Hello @ArnavBharti, You must be loosing the MM/ML/MN tags somewhere along the way. Could you check that the records have these tags after each step? If you can tell me the file formats of the outputs and inputs to the steps that could help me debug the problem. |
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Hello @ArnavBharti, Could you check that the reads have the MM/ML/MN tags at the end of each step? I have a feeling that your basecalled FASTQ does not have them. For your reference the tags I'm talking about are described in the SAM tags specification in section 1.7. |
Hi, could you tell if you check for these tags via text search or is there a tool. Because there exists 'MM' in the FASTq file upon a simple text search but I feel like I am probably missing something. |
Hi, |
Hello @ArtRand It would be nice if you could give insights on the same.
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The SAM/BAM tags as part of the FASTQ file format is not officially supported. The "support" for this is simply via the If you must use minimap2 ensure that you have the |
Hi,
As per 2, Is there a problem with the basecalled files? I'll try witth dorado aligner |
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Even with -y same issue |
Given that the awk line gives no results the issue is that you do not have modified base calls in your basecalls. Modified base calls are not available for FASTQ output from Dorado. If you output the default unmapped BAM the modified base calls will be there. You can also have Dorado perform the mapping while basecalling to avoid any of the minimap issues. I'm not sure what your downstream goals are with running nanopolish etc, but you can convert your unmapped BAM file to FASTQ with the |
Hello @marcus1487 The basecalling was done using trained RNN model i.e. res_dna_r941_min_modbases-all-context_v001 by using guppy v3.5.1. |
Hello @marcus1487 @ArtRand Art Note: Since the data came from the R9 flowcell, guppy was run. Therefore, in order to do the m6A modified basecalling, I utilised the following configuration file: Your opinions on the same would be greatly appreciated. Thanks |
I don't believe modified base output in FASTQ format is supported. You'll have to specify BAM output format in order to proceed from guppy basecalling. |
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Hello @marcus1487 @ArtRand It would be nice if you could help me with the above issue. Thanks |
Hello @PRIYANKA-22091995 and @ArnavBharti, You need to run the basecalling such that you get and unaligned BAM file as output (not FASTQ output). I believe that the |
@ArnavBharti @PRIYANKA-22091995, Any update on this? |
there is no option to put --bam out, and even after putting --bam out, it has only given fastq output. It would be nice to know any suggestion/input for the same. |
Hello @ArtRand |
@ArnavBharti @PRIYANKA-22091995, Any chance you could update guppy to at least |
Earlier was trying through guppy v0.6.2, but it failed with a error [guppy/error] The pipeline has shut down prematurely due to an error condition. So, then i moved to the previous version to do modified basecalling for m6A, but again it does not provide option with bam. |
I am getting this error while running modkit pileup:
modkit pileup <bam> <bed>
Procedure
I also ran modbam2bed. A file was formed by it gave methylation nan or 0
What could be the reason so?
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