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bvaldebenitom / SoloTE

GNU General Public License v3.0
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pandas error #25

Closed liuyuchenlab closed 11 months ago

liuyuchenlab commented 11 months ago

hi this is my bed file image and this is my bam file image they are all chr1,and ERROR: Requested column 3, but database file - only has fields 1 - 0.

i use this : python /disk5/lyc/biosoft/SoloTE_1.08/SoloTE_pipeline.py --bam possorted_genome_bam.bam --teannotation /disk5/lyc/reference/mouse/solote.bed --outputprefix e14 --outputdir /RNA_seq_1/lyc/project/lxm/solote/e14/ -t 1

could you tell me how to fix it? Thank you

bvaldebenitom commented 11 months ago

Hi @liuyuchenlab,

could you share the command line you used to generate the BED file? And the output of head on the RepeatMasker file you are using? It doesn't look like the BED file is formatted properly (first column is not chromosome, columns 2 and 3 are not both coordinates, nor column 4 begins with "chr")

liuyuchenlab commented 11 months ago

hi，i use this rmsk.txt from UCSC image convertRMOut_to_SoloTEinput.sh rmsk.txt solote.bed

liuyuchenlab commented 11 months ago

oh is not rmsk is out.gz