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bam file issue! #34

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g-s-2018 opened this issue Jan 7, 2023 · 0 comments
Open

bam file issue! #34

g-s-2018 opened this issue Jan 7, 2023 · 0 comments

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@g-s-2018
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g-s-2018 commented Jan 7, 2023

Hi, I am trying to run nanocaller but it does not recognize the bam file . I am getting this error msg: s)

~/data/minion/drs-output/drs-output-final/diversetools$

docker run genomicslab/nanocaller:3.0.0 NanoCaller \

--bam filtered-minmap_rsv_n1_9hpi-soreted.bam
--ref ~/data/minion/drs-output/drs-output-final/diversetools/subsample/KT992094.1.fasta --cpu 10 --snp_model SNP_MODEL

2023-01-07 22:30:52.732861: Starting NanoCaller.

NanoCaller command and arguments are saved in the following file: /app/args

[E::hts_open_format] Failed to open file "filtered-minmap_rsv_n1_9hpi-soreted.bam" : No such file or directory
Traceback (most recent call last):
File "/opt/conda/envs/nanocaller_env/bin/NanoCaller", line 178, in
run(args)
File "/opt/conda/envs/nanocaller_env/bin/NanoCaller", line 19, in run
regions_list=get_regions_list(args)
File "/opt/conda/envs/nanocaller_env/bin/nanocaller_src/utils.py", line 45, in get_regions_list
sam_file=pysam.Samfile(args.bam)
File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.cinit
File "pysam/libcalignmentfile.pyx", line 950, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file filtered-minmap_rsv_n1_9hpi-soreted.bam: No such file or directory

Any help would be much appreciated!

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