Hi, I ran into this issue when running the scafe.workflow.bk.solo workflow:
[2025-06-12 12:20] getting exon background count
Error: line number 311 of file /SCAFE/scripts/../resources/genome/hg38.gencode_v48/bed/exon.trnscpt_based.subtract_TSS_flank_250.bed.gz has 4 fields, but 6 were expected.
[2025-06-12 12:20] getting intron background count
Error: line number 387 of file /SCAFE/scripts/../resources/genome/hg38.gencode_v48/bed/intron.trnscpt_based.subtract_TSS_flank_250.bed.gz has 4 fields, but 6 were expected.
Inspecting the BED files above, I see for some rows the 4th column is abruptly interrupted (for instance ...;ENST00000831335.1;ENST00000831339.1;ENST0000) and 5th and 6th columns are lacking. The length for each of these rows is always the same, 4,095 characters.
Are you aware of any hardcoded limit for the length of an entry in the BED file?
I created the reference as described in the documentation with prep_genome using gencode.48 GTF and cCRE v4 for masking regions.
Thanks!
Hi, I ran into this issue when running the
scafe.workflow.bk.soloworkflow:Inspecting the BED files above, I see for some rows the 4th column is abruptly interrupted (for instance
...;ENST00000831335.1;ENST00000831339.1;ENST0000) and 5th and 6th columns are lacking. The length for each of these rows is always the same, 4,095 characters.Are you aware of any hardcoded limit for the length of an entry in the BED file?
I created the reference as described in the documentation with
prep_genomeusing gencode.48 GTF and cCRE v4 for masking regions.Thanks!