Closed markymarkfb90 closed 7 years ago
Hi Mark,
I suspect that RazerS3 is not properly configured. Did you add the Razer binary path to the config file and is RazerS3 working when calling it directly?
Also, could you perhaps post or send your config file?
Best, Benni
Hi Benni,
Thanks for the quick response. Please see my config file:
[mapping]
razers3= /Users/markg14/software/razers3 threads=16
[ilp]
solver=glpk threads=1
[behavior]
deletebam=true
unpaired_weight=0
use_discordant=false
Best wishes
Mark
razers3= /Users/markg14/software/razers3
this path has to point to the razers3 binary.
I would recommend using CBC (open source) or CPLEX (academic free license available) as ILP solver. These solvers also have multicore support.
Hope that resolves the problem.
Best, benni
Many thanks, all resolved and working now
great :-)
Hi! In case someone runs into the same error, I wanted to mention that in my case, razers3 worked perfectly when called alone, paths were correct, OptiType run successfully with the sample files etc, and it turned out that the bam files were not created because I was not allocating enough memory (around 18GB were needed for my samples). Cheers
Hi! In case someone runs into the same error, I wanted to mention that in my case, razers3 worked perfectly when called alone, paths were correct, OptiType run successfully with the sample files etc, and it turned out that the bam files were not created because I was not allocating enough memory (around 18GB were needed for my samples). Cheers
hi, I also can run successfully with the sample files, but I get the error when I run my fq.gz files. How do you allocate enough memory for your data?
Hi,
I was wondering if you could please help. Have attempted to install and run Optitype as per the guidance. Unfortunately this error is generated:
python /Users/markg14/software/OptiType-master/OptiTypePipeline.py -i ./test/rna/CRC_81_N_1_fished.fastq ./test/rna/CRC_81_N_2_fished.fastq --rna -v -o ./test/rna/
mapping with 4 threads...
0:00:02.83 Mapping CRC_81_N_1_fished.fastq to NUC reference...
0:00:04.49 Mapping CRC_81_N_2_fished.fastq to NUC reference...
0:00:05.09 Generating binary hit matrix. Traceback (most recent call last): File "/Users/markg14/software/OptiType-master/OptiTypePipeline.py", line 298, in
pos, read_details = ht.pysam_to_hdf(bam_paths[0])
File "/Users/markg14/software/OptiType-master/hlatyper.py", line 186, in pysam_to_hdf
sam = pysam.AlignmentFile(samfile, sam_or_bam)
File "pysam/libcalignmentfile.pyx", line 351, in pysam.libcalignmentfile.AlignmentFile.cinit (pysam/libcalignmentfile.c:5200)
File "pysam/libcalignmentfile.pyx", line 544, in pysam.libcalignmentfile.AlignmentFile._open (pysam/libcalignmentfile.c:7366)
IOError: file
./test/rna/2017_03_02_15_59_39/2017_03_02_15_59_39_1.bam
not foundAny help would be greatly appreciated.
Thank you
Mark