Error in generating a Snap file from a Bed file - IndexError: list index out of range

[joepelt]

Hi, I am trying to generate a Snap file from a Bed file.

Here is the code I enter:

snaptools snap-pre
--input-file=peaks.bed
--output-snap=demo.snap
--genome-name=mm10
--genome-size=mm10.chrom.sizes
--min-mapq=30
--min-flen=0
--max-flen=1000
--keep-chrm=TRUE
--keep-single=TRUE
--keep-secondary=False
--overwrite=True
--min-cov=100
--verbose=True

After I enter the code, the following output appears:

Traceback (most recent call last): File "/gpfs/commons/home/jpelt/.local/share/r-miniconda/envs/r-reticulate/bin/snaptools", line 38, in parse_args() File "/gpfs/commons/home/jpelt/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/snaptools/parser.py", line 144, in parse_args verbose=args.verbose) File "/gpfs/commons/home/jpelt/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/snaptools/snap_pre.py", line 206, in snap_pre if not snaptools.utilities.isQuerynameSorted(input_file, file_format): File "/gpfs/commons/home/jpelt/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/snaptools/utilities.py", line 118, in isQuerynameSorted return(isBedQuerynameSorted(fname)) File "/gpfs/commons/home/jpelt/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/snaptools/utilities.py", line 166, in isBedQuerynameSorted cur_barcode = str(item).split()[3]; IndexError: list index out of range

Does anyone have any idea of why my list index is out of range? Apologies in advance if this is very basic - I am a bit new to SnapATAC.

[wenhuihuang1979]

root@b02779cbbc78:/home/ec2-user/CD19_CAR_CD8Tcells/outs# snaptools snap-pre --input-f^C-output-snap=possorted_bam.snap.nsrt.snap --genome-name=hg38 --genome-size=/home/ec2-user/hg38.chrom.sizes --min-mapq=30 --min-flen=0 --max-flen=1000 --keep-chrm=TRUE --keep-single=TRUE --keep-secondary=False --overwrite=True --max-num=100000 --min-cov=100 --verbose=True root@b02779cbbc78:/home/ec2-user/CD19_CAR_CD8Tcells/outs# snaptools snap-pre --input-file=atat_CD19_CAR_CD8Tcells_fragments.srt.bed.gz --output-snap=possorted_bam.snap.nsrt.snap --genome-name=hg38 --genome-size=/home/ec2-user/hg38.chrom.sizes --min-mapq=30 --min-flen=0 --max-flen=1000 --keep-chrm=TRUE --keep-single=TRUE --keep-secondary=False --overwrite=True --max-num=100000 --min-cov=100 --verbose=True Traceback (most recent call last): File "/usr/local/bin/snaptools", line 38, in parse_args() File "/usr/local/lib/python2.7/dist-packages/snaptools/parser.py", line 144, in parse_args

verbose=args.verbose)

File "/usr/local/lib/python2.7/dist-packages/snaptools/snap_pre.py", line 224, in snap_pre barcode_dict = snaptools.snap.getBarcodesFromInput(input_file, file_format); File "/usr/local/lib/python2.7/dist-packages/snaptools/snap.py", line 177, in getBarcodesFromInput return getBarcodesFromBed(fname); File "/usr/local/lib/python2.7/dist-packages/snaptools/snap.py", line 256, in getBarcodesFromBed barcode = _read.split()[3].split(":")[0].upper(); IndexError: list index out of range

same here