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hello,
we are running nanodisco and we got this error at the characterize step.
nanodisco characterize -p 4 -b baumani -d analysis/merged_difference/baumani_difference.RDS -o analysis/baumani_motifs -m GATC,CCWGG,GCACNNNNNNGTT,AACNNNNNNGTGC -t nn -r reference_genome/Acinetobacter_baumannii_ATCC_BAA_747.fasta
[2022-09-13 14:11:52] Load supplied current differences.
[2022-09-13 14:11:52] Check current differences file version.
Models for Guppy version 6.3.4+cfaa134 is not yet available but we are working on it.
Motif characterization will still proceed with the default model but obtained results might not be optimal.
Additional information can be found in our GitHub repository.
[2022-09-13 14:11:52] Determine motif signature center.
[2022-09-13 14:11:52] Process GATC.
[2022-09-13 14:11:52] Tag GATC occurrences.
[2022-09-13 14:11:55] Score GATC modified position.
[2022-09-13 14:11:56] Process CCWGG.
[2022-09-13 14:11:56] Tag CCWGG occurrences.
[2022-09-13 14:11:57] Score CCWGG modified position.
[2022-09-13 14:11:57] Process GCACNNNNNNGTT.
[2022-09-13 14:11:57] Tag GCACNNNNNNGTT occurrences.
[2022-09-13 14:11:59] Score GCACNNNNNNGTT modified position.
[2022-09-13 14:11:59] Process AACNNNNNNGTGC.
[2022-09-13 14:11:59] Tag AACNNNNNNGTGC occurrences.
[2022-09-13 14:12:01] Score AACNNNNNNGTGC modified position.
Error in { :
task 1 failed - "arguments imply differing number of rows: 1, 0"
Calls: find.signature.center -> %do% -> <Anonymous>
Execution halted
So we had a look to the RDS File generated during the nanodisco difference step. It looks like this:
contig position dir strand N_wga N_nat mean_diff t_test_pval u_test_pval
9a03e25654c44fe8_1 1 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 5001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 10001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 15001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 20001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 25001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 30001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 35001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 40001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 45001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 50001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 55001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 60001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 65001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 70001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 75001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 80001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 85001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 90001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 95001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 100001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 105001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 110001 rev t 0 0 NA NA NA
9a03e25654c44fe8_1 115001 rev t 0 0 NA NA NA
We don't find any current differences detected. This could be a biological issue but what is also strange is that the positions reported are only every 5000 bp and only reverse sequences. Do you have an explanation for this?
do we have to set up a parameter in the difference step or upstream to have all the bases covered (1,2,3....).
thanks.
thanks for your kind help.
RB
The text was updated successfully, but these errors were encountered:
BioRB
changed the title
nanodisco characterize error task 1 failed
nanodisco characterize error task 1 failed and RDS file issue
Sep 13, 2022
Thank you for reaching out and sorry for the major delay. I hope you figure out the issue already but if not I'll try to help you sort it out.
The information contained in the difference file suggest that there was no data to process during nanodisco difference step. I would suggest loading the native and WGA .bam file from nanodisco preprocess in IGV to directly look at the data. Without more information, I would think that that the genome used do not match the strain/species sequenced or that your dataset is too shallow. Otherwise, an issue during nanodisco preprocess might have happened.
Feel free to reach back with more questions. I'll be more available in the future.
hello,
we are running nanodisco and we got this error at the characterize step.
So we had a look to the RDS File generated during the nanodisco difference step. It looks like this:
We don't find any current differences detected. This could be a biological issue but what is also strange is that the positions reported are only every 5000 bp and only reverse sequences. Do you have an explanation for this?
do we have to set up a parameter in the difference step or upstream to have all the bases covered (1,2,3....).
thanks.
thanks for your kind help.
RB
The text was updated successfully, but these errors were encountered: