I am re-doing an analysis on a new set of paired-end reads and can't seem to get passed the read edge trimming step. RNAEditor looks to have produced the XXXX.noSNPS.vcf file, but fails when it starts to remove the missmatches from the read edges. Have you encountered this problem before?
Thanks,
Michael
INFO: [Tue Mar 24 14:53:34 2020] Call variants [DONE] Duration [0:24:08.841354] INFO: [Tue Mar 24 15:17:43 2020] Parsing Variant Data from /stornext/General/data/academic/lab_vbcrc/Mick/Sequencing/2019_RNA_FACS_Pops/rnaEditor/Ba_RNA_R1/Ba_RNA_R1.vcf [DONE] Duration [0:00:50.722460] INFO: [Tue Mar 24 15:18:34 2020] Delete overlapps from /stornext/General/data/academic/lab_vbcrc/Mick/RNAEditor/RNAEditor/GRCM38/dbSNP.vcf [DONE] Duration [0:02:15.200438] INFO: [Tue Mar 24 15:20:49 2020] Print Variants to /stornext/General/data/academic/lab_vbcrc/Mick/Sequencing/2019_RNA_FACS_Pops/rnaEditor/Ba_RNA_R1/Ba_RNA_R1.noSNPs.vcf INFO: [Tue Mar 24 15:20:55 2020] remove Missmatches from the first 3 bp from read edges ERROR: RnaEditor Failed
Hi David @djhn75
I am re-doing an analysis on a new set of paired-end reads and can't seem to get passed the read edge trimming step. RNAEditor looks to have produced the XXXX.noSNPS.vcf file, but fails when it starts to remove the missmatches from the read edges. Have you encountered this problem before?
Thanks,
Michael
INFO: [Tue Mar 24 14:53:34 2020] Call variants [DONE] Duration [0:24:08.841354] INFO: [Tue Mar 24 15:17:43 2020] Parsing Variant Data from /stornext/General/data/academic/lab_vbcrc/Mick/Sequencing/2019_RNA_FACS_Pops/rnaEditor/Ba_RNA_R1/Ba_RNA_R1.vcf [DONE] Duration [0:00:50.722460] INFO: [Tue Mar 24 15:18:34 2020] Delete overlapps from /stornext/General/data/academic/lab_vbcrc/Mick/RNAEditor/RNAEditor/GRCM38/dbSNP.vcf [DONE] Duration [0:02:15.200438] INFO: [Tue Mar 24 15:20:49 2020] Print Variants to /stornext/General/data/academic/lab_vbcrc/Mick/Sequencing/2019_RNA_FACS_Pops/rnaEditor/Ba_RNA_R1/Ba_RNA_R1.noSNPs.vcf INFO: [Tue Mar 24 15:20:55 2020] remove Missmatches from the first 3 bp from read edges ERROR: RnaEditor Failed