Huanle
commented
3 years ago Hi @chaigsh ,
Can you try with the sam2tsv in the misc/ folder? Thanks.
Closed chaigsh closed 3 years ago
Huanle
commented
3 years ago Hi @chaigsh ,
Can you try with the sam2tsv in the misc/ folder? Thanks.
chaigsh
commented
3 years ago Hi @Huanle Yes, I try it. But other errors occured. When parameter "--number_cpus 1" was used, it is ok. However, it runs slowly. Thanks.
Huanle
commented
3 years ago Hi @chaigsh
What is the other error?
If it is too slow for you, can you split your bam file into smaller ones?
samtools view -hb big.bam {reference_sequence_id} > {reference_sequence_id} .bam would work.
Then try running it on the small bam files.
chaigsh
commented
3 years ago Hi @Huanle The parameter "--number_cpus 1" has no results returned. if not using "--number_cpus 1" , some errors occured.
/public/work/guoshi/bin/anaconda3/lib/python3.7/site-packages/dask/dataframe/utils.py:13: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
import pandas.util.testing as tm
/public/work/guoshi/data_processing/long-reads/nanopore/alignment/meswt_minimap_transcriptome.filt.sortTMP already exists, will overwrite it
/public/work/guoshi/data_processing/long-reads/nanopore/alignment/meswt_minimap_transcriptome.filt.sortTMP already exists, will overwrite it
Traceback (most recent call last):
File "/public/work/guoshi/bin/anaconda3/lib/python3.7/site-packages/dask/dataframe/utils.py", line 137, in raise_on_meta_error
yield
File "/public/work/guoshi/bin/anaconda3/lib/python3.7/site-packages/dask/dataframe/core.py", line 3583, in _emulate
return func(*_extract_meta(args, True), **_extract_meta(kwargs, True))
File "/public/work/guoshi/bin/anaconda3/lib/python3.7/site-packages/dask/dataframe/core.py", line 3567, in _extract_meta
return tuple([_extract_meta(_x, nonempty) for _x in x])
File "/public/work/guoshi/bin/anaconda3/lib/python3.7/site-packages/dask/dataframe/core.py", line 3567, in
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/public/work/guoshi/bin/EpiNano-master/Epinano_Variants.py", line 352, in
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/public/work/guoshi/bin/EpiNano-master/Epinano_Variants.py", line 352, in reset_index.
You have supplied a custom function and Dask is unable to determine the type of output that that function returns.
To resolve this please provide a meta= keyword. The docstring of the Dask function you ran should have more information.
Original error is below:
TypeError("new() got an unexpected keyword argument 'labels'")
Traceback:
File "/public/work/guoshi/bin/anaconda3/lib/python3.7/site-packages/dask/dataframe/utils.py", line 137, in raise_on_meta_error
yield
File "/public/work/guoshi/bin/anaconda3/lib/python3.7/site-packages/dask/dataframe/core.py", line 3583, in _emulate
return func(*_extract_meta(args, True), **_extract_meta(kwargs, True))
File "/public/work/guoshi/bin/anaconda3/lib/python3.7/site-packages/dask/dataframe/core.py", line 3567, in _extract_meta
return tuple([_extract_meta(_x, nonempty) for _x in x])
File "/public/work/guoshi/bin/anaconda3/lib/python3.7/site-packages/dask/dataframe/core.py", line 3567, in
Huanle
commented
3 years ago Hi @chaigsh ,
thanks for sharing the error message. can you also check the version of the packages that you have installed and see if they are the same as required ?
Huanle
commented
3 years ago Hi @chaigsh ,
can you try with the docker image that I mentioned in #94 ? I think that will solve your issue.
Hello,
When I use Epinano_Variants.py in EpiNano 1.2 to extract base-calling error features, an error occured. The code is below:
epinano="/public/work/guoshi/bin/EpiNano-master/" sam2tsv="/public/work/guoshi/bin/jvarkit-master/dist/sam2tsv.jar" ref="/public/data/guoshi/reference/mouse/GENCODE/" bamfile="/public/work/guoshi/data_processing/long-reads/nanopore/alignment/"
python ${epinano}Epinano_Variants.py -R ${ref}gencode.vM26.transcripts.fa --bam ${bamfile}meswt_minimap_transcriptome.filt.sort.bam --sam2tsv ${sam2tsv} --type t
The error is: Process Process-2: Traceback (most recent call last): File "/public/work/guoshi/bin/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/public/work/guoshi/bin/anaconda3/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/public/work/guoshi/bin/EpiNano-master/Epinano_Variants.py", line 44, in split_tsv_for_per_site_var_freq head = next(tsv) StopIteration
Thank you,
Regards