Closed ma-diroma closed 3 years ago
Hi,
I would like to generate admixfrog input from my BAM file, after generating reference.xz file.
This is the command launched
admixfrog-bam --bam sample_rmdup.sorted.bam --ref afr_nea_ref_samples.xz --random-read-sample --chroms 21 --deam-cutoff 3 --minmapq 30 --length-bin-size 35 --out sample.in.xz > admf_in.log 2> admf_in.err
However the process exits after a few seconds with this error
... [18:20:31]: Filter is {'deam_only': False, 'pos_in_read_cutoff': 2, 'min_length': 35, 'max_length': 1000, 'minq': 25, 'minmapq': 30, 'report_alleles': False} Traceback (most recent call last): File "/home/student6/anaconda3/envs/python38/bin/admixfrog-bam", line 8, in <module> sys.exit(bam()) File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/admixfrog/interface.py", line 141, in bam process_bam(**args) File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/admixfrog/bam.py", line 200, in process_bam cov = AdmixfrogInput( File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/admixfrog/bam.py", line 27, in __init__ raise NotImplementedError NotImplementedError
Could you please help me?
Best wishes, Maria Angela
Hi,
I would like to generate admixfrog input from my BAM file, after generating reference.xz file.
This is the command launched
admixfrog-bam --bam sample_rmdup.sorted.bam --ref afr_nea_ref_samples.xz --random-read-sample --chroms 21 --deam-cutoff 3 --minmapq 30 --length-bin-size 35 --out sample.in.xz > admf_in.log 2> admf_in.errHowever the process exits after a few seconds with this error
Could you please help me?
Best wishes, Maria Angela