Dear Developer
I'm sorry to bother you. I encountered a bug while using MEGAnE and I was hoping to get some assistance with it. I have been using your software for my plant data, and I have encountered an issue with the "call_genotype" steps. It is well known that transposons are a crucial component of plant genomes, and the study of Transposon Insertion Polymorphisms (TIP) is vital for understanding the contribution of transposons to phenotypes. The MEGAnE software provides an approach to explore the mechanisms involved, and it is believed that this method will undoubtedly find widespread application in future TIP research.
Due to the lack of comprehensive transposon annotation information for the species I am studying in the Dfam database, I conducted de novo annotation of transposable elements using EDTA. I have organized the annotation information for transposable elements as per the "Prepare a custom repeat library and annotation" steps you mentioned, manually formatting the TElib sequences (annotated from EDTA) into the format specified in the "Dfam_custom.rep" file. However, in the end, it still resulted in failure. I made efforts and reviewed the log files of the program, but still couldn't figure it out. Could you please provide some guidance or suggestions on how to resolve this bug? I would greatly appreciate any help you can provide. I have provided the program's runtime log in the attachment.
Here are the commands I used：
rule call_SNP_for_sample:
input:
BAMs='/public/home/weizhang/Call_SNPS/bam_V2/S478/S478_srt_q20_redup.bam',
referenceFasta='/cotton/Liuzhenping/Pan-genome/AD1-genomes/HC04/HC04.chr.fa',
KmerFile='/public/home/zpliu/TIP/MEGAnE/step_00.megane_kmer_set/HC04.chr.mk',
#* path to blastdb of reference genome
fadb='/public/home/zpliu/TIP/MEGAnE/Blast_database.nin',
#* path to repeat library
rep='/public/home/zpliu/TIP/MEGAnE/RepeatAnnotate/HC04_chr_EDTA.rep',
#* path to repeat annotation
repout='/public/home/zpliu/TIP/MEGAnE/RepeatAnnotate/HC04_chr_adjust.fa.mod.EDTA.intact.fa.out',
#* a list of mobile element with polyA tail
pA_ME="/public/home/zpliu/TIP/MEGAnE/RepeatAnnotate/ME_with_pA.txt",
#* a list of non-mobile element headers
repremove="/public/home/zpliu/TIP/MEGAnE/RepeatAnnotate/non_ME_rep.txt",
#* specify a list of chromosomes to be analyzed
mainchr ="/public/home/zpliu/TIP/MEGAnE/RepeatAnnotate/main_chrs.txt"
threads: 2
resources:
mem_mb=15000
params:
bindPath="/cotton/Liuzhenping/Pan-genome/AD1-genomes/HC04,/public/home/weizhang/Call_SNPS/bam_V2/,/public/home/zpliu/TIP/MEGAnE/",
SampleName='S478',
fadb='/public/home/zpliu/TIP/MEGAnE/Blast_database'
shell:
"""
module load Singularity/3.1.1
singularity exec -B {params.bindPath} MEGAnE.sif call_genotype \
-i {input.BAMs} \
-fa {input.referenceFasta} \
-mk {input.KmerFile} \
-sample_name {params.SampleName} \
-lowdep \
-p {threads} \
-fadb {params.fadb} \
-rep {input.rep} \
-repout {input.repout} \
-pA_ME {input.pA_ME} \
-repremove {input.repremove} \
-mainchr {input.mainchr} \
-no_sex_chr \
-keep \
-outdir {params.SampleName}
"""
Dear Developer I'm sorry to bother you. I encountered a bug while using MEGAnE and I was hoping to get some assistance with it. I have been using your software for my plant data, and I have encountered an issue with the "call_genotype" steps. It is well known that transposons are a crucial component of plant genomes, and the study of Transposon Insertion Polymorphisms (TIP) is vital for understanding the contribution of transposons to phenotypes. The MEGAnE software provides an approach to explore the mechanisms involved, and it is believed that this method will undoubtedly find widespread application in future TIP research. Due to the lack of comprehensive transposon annotation information for the species I am studying in the Dfam database, I conducted de novo annotation of transposable elements using EDTA. I have organized the annotation information for transposable elements as per the "Prepare a custom repeat library and annotation" steps you mentioned, manually formatting the TElib sequences (annotated from EDTA) into the format specified in the "Dfam_custom.rep" file. However, in the end, it still resulted in failure. I made efforts and reviewed the log files of the program, but still couldn't figure it out. Could you please provide some guidance or suggestions on how to resolve this bug? I would greatly appreciate any help you can provide. I have provided the program's runtime log in the attachment.
Here are the commands I used：
Some result file in call genotype step:
Thank you for your time and attention.
Best regards, zpliu
for_debug.log