Are non-human reference genomes supported? about hatchet HOT 10 CLOSED

hatchet run hatchet.ini

hatchet count-reads -N ${NORMAL} -T ${PRIME} -b 25kb -g ${REF} -j 16 -O XX -o XpX -t total_read.counts --verbose

WARNING: a chromosome named either 1 or a variant of CHR1 cannot be found in the normal BAM file
WARNING: a chromosome named either 2 or a variant of CHR2 cannot be found in the normal BAM file
WARNING: a chromosome named either 3 or a variant of CHR3 cannot be found in the normal BAM file
WARNING: a chromosome named either 4 or a variant of CHR4 cannot be found in the normal BAM file
WARNING: a chromosome named either 5 or a variant of CHR5 cannot be found in the normal BAM file
WARNING: a chromosome named either 6 or a variant of CHR6 cannot be found in the normal BAM file
WARNING: a chromosome named either 7 or a variant of CHR7 cannot be found in the normal BAM file
WARNING: a chromosome named either 8 or a variant of CHR8 cannot be found in the normal BAM file
WARNING: a chromosome named either 9 or a variant of CHR9 cannot be found in the normal BAM file
WARNING: a chromosome named either 10 or a variant of CHR10 cannot be found in the normal BAM file
WARNING: a chromosome named either 11 or a variant of CHR11 cannot be found in the normal BAM file
WARNING: a chromosome named either 12 or a variant of CHR12 cannot be found in the normal BAM file
WARNING: a chromosome named either 13 or a variant of CHR13 cannot be found in the normal BAM file
WARNING: a chromosome named either 14 or a variant of CHR14 cannot be found in the normal BAM file
WARNING: a chromosome named either 15 or a variant of CHR15 cannot be found in the normal BAM file
WARNING: a chromosome named either 16 or a variant of CHR16 cannot be found in the normal BAM file
WARNING: a chromosome named either 17 or a variant of CHR17 cannot be found in the normal BAM file
WARNING: a chromosome named either 18 or a variant of CHR18 cannot be found in the normal BAM file
WARNING: a chromosome named either 19 or a variant of CHR19 cannot be found in the normal BAM file
WARNING: a chromosome named either 20 or a variant of CHR20 cannot be found in the normal BAM file
WARNING: a chromosome named either 21 or a variant of CHR21 cannot be found in the normal BAM file
WARNING: a chromosome named either 22 or a variant of CHR22 cannot be found in the normal BAM file
Traceback (most recent call last):
  File "/mnt/sequence/jurban/software/conda/anaconda3/envs/hatchet/bin/hatchet", line 33, in <module>
    sys.exit(load_entry_point('hatchet==0.4.7', 'console_scripts', 'hatchet')())
  File "/mnt/sequence/jurban/software/conda/anaconda3/envs/hatchet/lib/python3.7/site-packages/hatchet/__main__.py", line 65, in main
    globals()[command](args)
  File "/mnt/sequence/jurban/software/conda/anaconda3/envs/hatchet/lib/python3.7/site-packages/hatchet/utils/count_reads.py", line 16, in main
    args = ap.parse_count_reads_arguments(args)
  File "/mnt/sequence/jurban/software/conda/anaconda3/envs/hatchet/lib/python3.7/site-packages/hatchet/utils/ArgParsing.py", line 277, in parse_count_reads_arguments
    chromosomes = extractChromosomes(samtools, normal, samples)
  File "/mnt/sequence/jurban/software/conda/anaconda3/envs/hatchet/lib/python3.7/site-packages/hatchet/utils/ArgParsing.py", line 520, in extractChromosomes
    if len(chrm) == 0 and len(no_chrm) == 0: raise ValueError("No chromosomes found in the normal BAM")
ValueError: No chromosomes found in the normal BAM

conda create -n hatchet -c bioconda hatchet
conda activate hatchet
conda install tabix picard mosdepth
conda install shapeit -c dranew
conda install -c gurobi gurobi

505 def extractChromosomes(samtools, normal, tumors, reference=None):
    506     # Read the names of sequences in normal BAM file
    507     normal_sq = getSQNames(samtools, normal[0])
    508 
    509     # Extract only the names of chromosomes in standard formats
    510     chrm = set()
    511     no_chrm = set()
    512     for i in range(1, 23):
    513         if str(i) in normal_sq:
    514             no_chrm.add(str(i))
    515         elif "chr" + str(i) in normal_sq:
    516             chrm.add("chr" + str(i))
    517         else:
    518             sys.stderr.write("WARNING: a chromosome named either {} or a variant of CHR{} cannot be found in the normal BAM file\n".format(i, i))
    519 
    520     if len(chrm) == 0 and len(no_chrm) == 0: raise ValueError("No chromosomes found in the normal BAM")