KeyError: "sequence 'chr22' not present" for rgt-motifanalysis matching

[hyjforesight]

Hello RGT, Thanks for developing this amazing package. I met the error KeyError: "sequence 'chr22' not present" when following the full-site test tutorial here (http://www.regulatory-genomics.org/motif-analysis/introduction/). Could you please help me with this issue? Thanks! Best, YJ

cd RGT_MotifAnalysis_FullSiteTest
rgt-motifanalysis matching --input-files input/regions_K562.bed input/background.bed --organism hg19
>> output location: /home/hyjforesight/RGT_MotifAnalysis_FullSiteTest/match

>> genome: hg19
>> pseudocounts: 1.0
>> fpr threshold: 0.0001

>> loading input files..
>>> regions_K562, 358 regions
>>> background, 515 regions

>> loading motif databases..
>>> jaspar_vertebrates

>> motifs loaded: 746

>> matching [regions_K562], 358 regions... Traceback (most recent call last):
  File "/home/hyjforesight/.local/bin/rgt-motifanalysis", line 8, in <module>
    sys.exit(main())
  File "/home/hyjforesight/.local/lib/python3.9/site-packages/rgt/motifanalysis/Main.py", line 58, in main
    args.func(args)
  File "/home/hyjforesight/.local/lib/python3.9/site-packages/rgt/motifanalysis/Match.py", line 399, in main
    sequence = str(genome_file.fetch(genomic_region.chrom, genomic_region.initial, genomic_region.final))
  File "pysam/libcfaidx.pyx", line 303, in pysam.libcfaidx.FastaFile.fetch
KeyError: "sequence 'chr22' not present"

[fabio-t]

Hi, have you prepared the genomes beforehand? http://www.regulatory-genomics.org/rgt/rgt-data-folder/

[hyjforesight]

hello @fabio-t Thanks for the response. Yes, I did python ~/rgtdata/setupGenomicData.py --hg19, but the error continues.

[hyjforesight]

hello @fabio-t Is it because it's not hg19? Thanks! Best, YJ