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nanoporetech
error in getting files
I am running tombo resquiggle. I have given the path for my fast5 file and reference genome. After loading minimap2 reference there is an error in getting files.
Errors: Reads do not to contain basecalls. The provided directory is not the directory.
(myenv) anban@LAPTOP-ALFC6RCO:~$ ls
fast5dir fastqdir hg38.analysisSet.fa
(myenv) anban@LAPTOP-ALFC6RCO:~$ tombo resquiggle fast5dir/ hg38.analysisSet.fa
[10:04:53] Loading minimap2 reference.
[10:10:47] Getting file list.
******************** ERROR ********************
Reads do not to contain basecalls. Check --basecall-group option if basecalls are stored in non-standard location or use tombo preprocess annotate_raw_with_fastqs to add basecalls from FASTQ files to raw FAST5 files.
fast5dir contains all my fast5 files fastqdir has the respective fastq files hg38.analysisSet.fa is my reference genome file [fasta]
Do let me know what am I missing, which is causing this issue?
It looks as though the basecalls are not found within the FAST5 files. Have you run the tombo preprocess annotate_raw_with_fastqs command? See more documentation on this preprocessing step here: https://nanoporetech.github.io/tombo/resquiggle.html.
It looks as though the basecalls are not found within the FAST5 files. Have you run the
tombo preprocess annotate_raw_with_fastqscommand? See more documentation on this preprocessing step here: https://nanoporetech.github.io/tombo/resquiggle.html.
I have run the tombo preprocess annotate_raw_with_fastqs command, but there are some errors:
tombo preprocess annotate_raw_with_fastqs --fast5-basedir 0(directory with some fast5s) --fastq-filenames nanopore_data *.fastq
[17:18:13] Preparing reads and extracting read identifiers.
****** WARNING ****** Basecalls exsit in specified slot for some reads. Set --overwrite option to overwrite these basecalls.
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 8000/8000 [00:03<00:00, 2653.47it/s]
[17:18:16] Annotating FAST5s with sequence from FASTQs.
****** WARNING ****** Some FASTQ records contain read identifiers not found in any FAST5 files or sequencing summary files.
0it [00:00, ?it/s]
[17:18:16] Added sequences to a total of 0 reads.
What seems to be the problem,please?
It looks as though the basecalls are not found within the FAST5 files. Have you run the
tombo preprocess annotate_raw_with_fastqscommand? See more documentation on this preprocessing step here: https://nanoporetech.github.io/tombo/resquiggle.html.
I have run the tombo preprocess annotate_raw_with_fastqs command, but there are some errors:
tombo preprocess annotate_raw_with_fastqs --fast5-basedir 0(directory with some fast5s) --fastq-filenames nanopore_data *.fastq
[17:18:13] Preparing reads and extracting read identifiers.
****** WARNING ****** Basecalls exsit in specified slot for some reads. Set --overwrite option to overwrite these basecalls.
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 8000/8000 [00:03<00:00, 2653.47it/s]
[17:18:16] Annotating FAST5s with sequence from FASTQs.
****** WARNING ****** Some FASTQ records contain read identifiers not found in any FAST5 files or sequencing summary files.
0it [00:00, ?it/s]
[17:18:16] Added sequences to a total of 0 reads.
What seems to be the problem,please?
As the warning messages indicate, it appears the FAST5 files have basecalls in them already. Either add the --overwrite flag or proceed to the resquiggle step with the basecalls currently found in the FAST5s.