WARNING 2020-10-20 17:26:48,369 haplo_1_1167112_1167113 could not pileup for region: 1:1167103 WARNING 2020-10-20 17:27:46,108 1_1167103_1167198_None_None warning: no mate for hsa-mir-200b_MI0000342-s11000

[andreiaamaral]

Dear Adam,
I am trying to use bamsurgeon for the first time. I want to generate sequencing data of regions corresponding to miRNAs with snvs. I have struggled but I keep receiving these warning messages.

my command is
sudo addsnv.py --varfile /data/ref_genome_human/GRCh38_miRNAs_mature_noIDS.bed --bamfile /data/isomir_testing_varying_read_lenght/sample1_all_sizes_sim22_RG_sorted.bam --reference /data/ref_genome_human/GRCh38.dna.fa --picardjar /home/andreiaamaral/Documents/software/picard-tools-1.131 --outbam testregion_mut.bam

I have checked the bam file with picard and no errors are created. This bam file is from a simulated dataset using ART. To generate data of small-RNA-seq. Now I need to simulate a set with SNVs and another with insertions.

the warnings that I get are:

WARNING 2020-10-20 17:26:48,369 haplo_1_1167112_1167113 could not pileup for region: 1:1167103
WARNING 2020-10-20 17:27:46,108 1_1167103_1167198_None_None warning: no mate for hsa-mir-200b_MI0000342-s11000
WARNING 2020-10-20 17:28:44,313 1_1167103_1167198_None_None warning: no mate for hsa-mir-200b_MI0000342-s1994
WARNING 2020-10-20 17:30:01,145 1_1167103_1167198_None_None warning: no mate for hsa-mir-200b_MI0000342-s1992
WARNING 2020-10-20 17:30:12,965 1_1167103_1167198_None_None warning: no mate for hsa-mir-200b_MI0000342-s1991
WARNING 2020-10-20 17:30:24,451 1_1167103_1167198_None_None warning: no mate for hsa-mir-200b_MI0000342-s1990
WARNING 2020-10-20 17:30:35,971 1_1167103_1167198_None_None warning: no mate for hsa-mir-200b_MI0000342-s1988
WARNING 2020-10-20 17:30:47,653 1_1167103_1167198_None_None warning: no mate for hsa-mir-200b_MI0000342-s1986

and so on
cam you try to help?
thanks
Andreia