You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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!
The text was updated successfully, but these errors were encountered:
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 \
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 directoryAny help would be much appreciated!
The text was updated successfully, but these errors were encountered: