could not open alignment file
tamlav opened this issue · comments
Hi,
I want to use optitype.
I run:
sudo docker pull fred2/optitype
which works fine, but when run:
sudo docker run -v /path to folder:/data/ -t fred2/optitype -i myfile.fastq -d -o /data/
I got error:
[E::hts_open_format] Failed to open file /data/2022_05_31_04_55_51/2022_05_31_04_55_51_1.bam
Traceback (most recent call last):
File "/usr/local/bin/OptiType/OptiTypePipeline.py", line 358, in
pos, read_details = ht.pysam_to_hdf(bam_paths[0])
File "/usr/local/bin/OptiType/hlatyper.py", line 186, in pysam_to_hdf
sam = pysam.AlignmentFile(samfile, sam_or_bam)
File "pysam/libcalignmentfile.pyx", line 728, in pysam.libcalignmentfile.AlignmentFile.cinit
File "pysam/libcalignmentfile.pyx", line 918, in pysam.libcalignmentfile.AlignmentFile._open
IOError: [Errno 2] could not open alignment file /data/2022_05_31_04_55_51/2022_05_31_04_55_51_1.bam
: No such file or directory
It do create the folder in data.
I tried different folders as path including root file.
I tried to find help in different places.
any help?
thanks
I have the same error,did you know how to fix it?
thanks