different version different error about methplotlib HOT 19 CLOSED

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Can you check that the gff file you are using uses "16" as a chromosome identifier?

from methplotlib.

Hi @wdecoster ,

thanks for the quick response. I have an issue with my cluster now but ı wanna say that this .gff file works fine with version 0.8. Also, I have different gff3, gff and gtf. files and all dont work for both versions (0.17 and 0.20). many thanks.

best.

from methplotlib.

I just pushed a new version to PyPI, v0.20.1, can you see if that solves anything?
I should really rewrite the GFF/GTF parsing code but I have no time.

from methplotlib.

Hi @wdecoster,

sorry for the late return. now its works with nanopolish output. I am also working with the megalodon output and ı couldn't able to run the cram file in methplotlib and ı am getting the error below. do you have any help with that? thanks for your help.

The log file
2022-04-20 12:01:28,810 methplotlib 0.20.1 started.
2022-04-20 12:01:28,810 Python version is: 3.7.13 (default, Mar 29 2022, 02:18:16) [GCC 7.5.0]
2022-04-20 12:01:28,810 Arguments are: Namespace(bed='modified_bases.5mC.bed', binary=False, dotsize=4, example=False, fasta=None, gtf='GRCh38genomic.gff', methylation=['mapping_sorted.cram'], minqual=20, names=['calls'], outfile=None, qcfile=None, simplify=False, smooth=5, split=False, static=None, store=False, window='16:10,000,000-12,000,000')
2022-04-20 12:01:28,813 Processing 16_10000000_11000000
2022-04-20 12:01:28,822 File mapping_sorted.cram is of type bam
2022-04-20 12:01:28,995 Collected methylation data for 0 datasets
2022-04-20 12:01:29,575 Created QC plots
2022-04-20 12:01:29,575 Prepared methylation traces.
2022-04-20 12:01:29,575 Making browser in overlaying mode.

The error:
Traceback (most recent call last):
File "/cluster/lrcfs/ftiras/ftiras_env/envs/Methplotlib17/bin/methplotlib", line 10, in
sys.exit(main())
File "/cluster/lrcfs/ftiras/ftiras_env/envs/Methplotlib17/lib/python3.7/site-packages/methplotlib/methplotlib.py", line 36, in main
minqual=args.minqual, # only for input in bam/cram format
File "/cluster/lrcfs/ftiras/ftiras_env/envs/Methplotlib17/lib/python3.7/site-packages/methplotlib/methplotlib.py", line 94, in meth_browser
if meth_traces.types[0] == 'nanopolish_freq':
IndexError: list index out of range

many thanks. great days,

Fatih.

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What is the output of the following?

samtools view mapping_sorted.cram 16:10,000,000-12,000,000 | wc -l

from methplotlib.

hi @wdecoster ,

thanks for your answer. ı got this after typing your advice. Also, ı have latest version of samtools which is 1.15. many thanks. best wishes
samtools: /cluster/lrcfs/2397405/ftiras_env/bin/../lib/libtinfow.so.6: no version information available (required by samtools)
samtools: /cluster/lrcfs/2397405/ftiras_env/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /cluster/lrcfs/2397405/ftiras_env/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
266

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Do you think you can share that file?

from methplotlib.

hi @wdecoster yes I can but the github dont support to upload the file do you know how can ı upload it ? thanks.

from methplotlib.

How large is the file in megabytes or gigabytes?

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252.630 kb

from methplotlib.

Is that 252Mb or 252 kb? Not sure what your decimal separator is.

from methplotlib.

sorry, my bad ı am using a different separation technique. it is 246 MB (258.692.244 bayt)

from methplotlib.

Okay, can you try uploading to https://www.dropbox.com/request/lfyAHhYE5nslcjMWmgc2 ?

from methplotlib.

Hi @wdecoster ,

thanks for sending link. I uploaded the mapping_sorted.cram file

from methplotlib.

I don't see any modified nucleotides in this file. The information simply isn't there. How was this file generated?

from methplotlib.

Hi @wdecoster ,

first, we used megalodon for generating cram file. then samtools was used for sorted and indexing. Also, we generated some data from similar data with nanopolish package. thanks.

megalodon command: "qsub -pe smp 40 -jc long -M [email protected] -m ae -cwd -b y -R y megalodon Firstrun61fast5subset/ --reference wholegenome.fasta --outputs basecalls mappings mods --mappings-format cram --sort-mappings --processes 40 --guppy-server-path /cluster/lrcfs/2397405/bin/ont-guppy-cpu-6.0.1/bin/guppy_basecall_server --guppy-params "-d /cluster/lrcfs/2397405/bin/rerio/basecall_models/ --num_callers 40" --guppy-timeout 400 --guppy-config res_dna_r941_min_modbases_5mC_CpG_v001.cfg --overwrite --output-directory megalodon_results_secondcram61seconda "

samtools command:" samtools index mappings.cram
samtools sort mappings.cram > mapping_sorted.cram
samtools index mapping_sorted.cram"

from methplotlib.

Well; this is not a problem of methplotlib, there are no modifications in this bam file.

from methplotlib.

Hi @wdecoster,

thanks for your help, we are working on that.

Kind Regards.

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