tleonardi/nanocompore_pipeline

Nextflow pipeline for nanocompore analysis

nanocompore_pipeline's Issues

Error with nanocompore sampcomp

Hi @tleonardi ,

I ran into an error with this command:

nanocompore sampcomp --file_list1 bc1.evnaln.collapse/out_eventalign_collapse.tsv,bc2.evnaln.collapse/out_eventalign_collapse.tsv,bc3.evnaln.collapse/out_eventalign_collapse.tsv --file_list2 bc4.evnaln.collapse/out_eventalign_collapse.tsv --label1 KO --label2 WT --fasta yeast_rRNA_ref.fa --outpath ./results --overwrite --nthreads 8

error message:

Initialising SampComp and checking options
Only 1 replicate found for condition WT
This is not recommended. The statistics will be calculated with the logit method
Initialising Whitelist and checking options
Reading eventalign index files
References found in index: 4
Filtering out references with low coverage
References remaining after reference coverage filtering: 2
Starting data processing
M 0%| | 0/2 [00:00<?, ? Processed References/s]M 0%| | 0/2 [00:00<?, ? Processed References/s]
Loading SampCompDB
Traceback (most recent call last):
File "/nfs/users2/enovoa/hliu/mygit/nanocompare/bin/nanocompore", line 8, in
sys.exit(main())
File "/nfs/users2/enovoa/hliu/mygit/nanocompare/lib/python3.6/site-packages/nanocompore/main.py", line 139, in main
args.func(args)
File "/nfs/users2/enovoa/hliu/mygit/nanocompare/lib/python3.6/site-packages/nanocompore/main.py", line 174, in sampcomp_main
db = s()
File "/nfs/users2/enovoa/hliu/mygit/nanocompare/lib/python3.6/site-packages/nanocompore/SampComp.py", line 268, in call
log_level=self.__log_level)
File "/nfs/users2/enovoa/hliu/mygit/nanocompare/lib/python3.6/site-packages/nanocompore/SampCompDB.py", line 82, in init
raise NanocomporeError("The result database is empty")
nanocompore.common.NanocomporeError: The result database is empty
Initialising SampComp and checking options
Only 1 replicate found for condition WT
This is not recommended. The statistics will be calculated with the logit method
Initialising Whitelist and checking options
Reading eventalign index files
References found in index: 4
Filtering out references with low coverage
References remaining after reference coverage filtering: 2
Starting data processing
M 0%| | 0/2 [00:00<?, ? Processed References/s]M 0%| | 0/2 [00:00<?, ? Processed References/s]
Loading SampCompDB
Traceback (most recent call last):
File "/nfs/users2/enovoa/hliu/mygit/nanocompare/bin/nanocompore", line 8, in
sys.exit(main())
File "/nfs/users2/enovoa/hliu/mygit/nanocompare/lib/python3.6/site-packages/nanocompore/main.py", line 139, in main
args.func(args)
File "/nfs/users2/enovoa/hliu/mygit/nanocompare/lib/python3.6/site-packages/nanocompore/main.py", line 174, in sampcomp_main
db = s()
File "/nfs/users2/enovoa/hliu/mygit/nanocompare/lib/python3.6/site-packages/nanocompore/SampComp.py", line 268, in call
log_level=self.__log_level)
File "/nfs/users2/enovoa/hliu/mygit/nanocompare/lib/python3.6/site-packages/nanocompore/SampCompDB.py", line 82, in init
raise NanocomporeError("The result database is empty")
nanocompore.common.NanocomporeError: The result database is empty

Can you help to fix it? Thanks a lot!

Nanopolish Comp error

Hello,

I am getting an error when running the nextflow pipeline.

This is my .command.sh that the error message told me to check out:

cat guppy/*.fastq > basecalled.fastq
nanopolish index -s guppy/sequencing_summary.txt -d 'raw_data' basecalled.fastq
mkdir -p nanopolishcomp/
       nanopolish eventalign -t 31 --reads basecalled.fastq --bam minimap.filt.sort.bam --genome reference_transcriptome.fa --samples --print-read-names --scale-events | NanopolishComp Eventalign_collapse -t 31 -o ./nanopolishcomp

here was the .command.log output

NanopolishComp.common.NanopolishCompError: Traceback (most recent call last):
  File "~/conda_compore/lib/python3.6/site-packages/NanopolishComp/Eventalign_collapse.py", line 241, in _write_output
    with open (self.output_fn, "w") as output_fp,\
IsADirectoryError: [Errno 21] Is a directory: './nanopolishcomp'

Any idea on how I can solve this?

thanks,

Matt

Issue with dataset and Nanopolish resquiggling

Hi!

We're currently working on familiarizing ourselves with the Nanocompore pipeline by reanalyzing the data provided in your 2019 paper (the ENA .fastq files, as well as .cram files converted to fast5 with ont2cram). When we reached the final resquiggling step, we found that there was a low number of reads, with all of them listed as "bad fast5." We were able to get in contact with Logan in your lab, who helped us see that all the Us and Ts appeared as Ns in the fastq reads, and also that the ERR3719134 fast5 file could not be basecalled because of a 'flow_cell_id' not found error.

I know we've also been in contact via email, but posting here as well for more direct communication! Thanks for all your help!

Extend transcripts by a small amount on both sides

Before creating the reference fasta file it's probably a good idea to extend transcripts slightly on both sides.

libssh2==1.8.0=h5b517e9_3

While trying to create a conda environment from conda_env.yaml following error appears
ResolvePackageNotFound:

• libssh2==1.8.0=h5b517e9_3

Which reference to use for dRNA-seq

Hi,

I'm trying to analyse direct RNA seq results for m6A modification detection

Does the pipeline create reference transcriptome itself from the reference genome and .gtf file which are defined in the nextflow.config?
I am a little confused because in the Nanocompore documentation it says to use reference transcriptome (not genome) and then in the nextflow.cofing file one has to provide a reference genome.
If I provide a reference transcriptome in the nextflow.config file, then I can not create .fa.fai file since the transcriptome file does not have chromosome information in its header.

Thank You

is this pipeline a conda package

Hi,
is the installation of pipeline available as a conda package (conda install)? I could only find the installation via pypi (pip install)

Release a stable version

Make a release for the Nanocompore preprint

Missing pycoQC

pycoQC is not listed as a dependency in the conda environment

using spike in as control for modification detection

Hi,

May I ask if your tool support control data which was introduced as spike-in into the wild type sample.

Best,

Leily

Impose specific versions for all dependencies

The version number of pycoQC, NanopolishComp and Bedparse is not indicated in the singularity recipe. This would be nice for a stable release of the pipeline

Add Guppy

Add support for optionally using Guppy to basecall instead of Albacore