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zhqingit / giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
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Error: Can't find snv in SNV list #45

Open zambofd opened 6 years ago

zambofd commented 6 years ago

Hi qing, when i used the command: giremi -f Sus_scrofa.Sscrofa10.2.dna.toplevel.fa -l H.txt -p 1 -s 0 -o H.RNAE.lst brain.sort.rmdup.bam, I got the problem like that: [mpileup] 1 samples in 1 input files error:Can't find snv in SNV list:13:118446201:+

kjshan commented 1 year ago

I have the same problem. have you dealed with it

kjshan commented 1 year ago

/gpfs2/shankj/RNAediting/shankj/DNA_BaseCount/Loliolus_beka.GIREMI.vcf

TRINITY_DN10001_c2_g1_i2 81 82 TRINITY_DN10001_c2_g1_i2 0 - TRINITY_DN10001_c2_g1_i2 82 83 TRINITY_DN10001_c2_g1_i2 0 - TRINITY_DN10001_c2_g1_i2 84 85 TRINITY_DN10001_c2_g1_i2 0 - TRINITY_DN10001_c2_g1_i2 87 88 TRINITY_DN10001_c2_g1_i2 0 -

/gpfs2/shankj/software/giremi-master/giremi --fasta-ref /gpfs2/shankj/RNAediting/DNA_Corrected_Trinity_longest/Loliolus_beka.DNA.Corrected.fas -l /gpfs2/shankj/RNAediting/shankj/DNA_BaseCount/Loliolus_beka.GIREMI.vcf -o /gpfs2/shankj/RNAediting/shankj/DNA_BaseCount/Loliolus_beka.GIREMI.result.txt -p 0 -s 0 /gpfs2/shankj/RNAediting/shankj/RNA_bwa/Loliolus_beka_armnervecord.RNA.bwa.sort.bam &

[shankj@21:40:03 ~][mpileup] 1 samples in 1 input files error:Can't find snv in SNV list:TRINITY_DN20911_c0_g1_i`3f:673:1

However， only TRINITY_DN20911_c0_g1_i1 in the /gpfs2/shankj/RNAediting/shankj/DNA_BaseCount/Loliolus_beka.GIREMI.vcf TRINITY_DN20911_c0_g1_i1 19 20 TRINITY_DN20911_c0_g1_i1 0 - TRINITY_DN20911_c0_g1_i1 20 21 TRINITY_DN20911_c0_g1_i1 0 - TRINITY_DN20911_c0_g1_i1 69 70 TRINITY_DN20911_c0_g1_i1 0 - TRINITY_DN20911_c0_g1_i1 672 673 TRINITY_DN20911_c0_g1_i1 0 -