OptiType Fails to Open Intermediate BAM File

[valeriaMCuevas]

Hi everyone,

I am trying to run OptiType. I have followed the pre-filtering steps described in this link, but when I input the FASTQ files to run the program, I receive the following error message:

0:00:00.70 Mapping input_R1.fastq.gz to NUC reference...
0:00:00.73 Mapping input_R2.fastq.gz to NUC reference...
0:00:00.89 Generating binary hit matrix.
Traceback (most recent call last):
File "/path/to/OptiTypePipeline.py", line 309, in
pos, read_details = ht.pysam_to_hdf(bam_paths[0])
File "/path/to/hlatyper.py", line 186, in pysam_to_hdf
sam = pysam.AlignmentFile(samfile, sam_or_bam)
File "pysam/calignmentfile.pyx", line 311, in pysam.calignmentfile.AlignmentFile.cinit (pysam/calignmentfile.c:4929)
File "pysam/calignmentfile.pyx", line 480, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:6905)
IOError: file /path/to/output_directory/2024_09_09_22_41_15_1.bam not found

The command I am using is as follows:

OptiTypePipeline.py -i /path/to/fastq_files/sample_R1.fastq.gz /path/to/fastq_files/sample_R2.fastq.gz
--rna
--enumerate 5
--verbose
--prefix sample
--outdir /path/to/output_directory
--config /path/to/config_file

confi.ini file:

**[mapping]
razers3=/path/to/razers3
threads=1

[ilp]
solver=glpk
threads=1

[behavior]

deletebam=false
unpaired_weight=0.2
use_discordant=false**

These are the programs with the versions I am using:

1. razers/3.4
2. optitype/1.3.4
3. cbc/2.10.3
4. htslib/1.2.1
5. samtools/1.2
6. anaconda2/4.3.1
7. hdf5/1.8.19

I've come across a few suggested solutions for this issue, and I've tried most of them, but I'm still unable to resolve the problem. Has anyone encountered this before or know how to fix it? Any help would be greatly appreciated. Thank you in advance!

Valeria