Issue with no Hap1 and Hap2 file

[masterzhen119]

Hello. I am using this simulation tool and found that the tool need simulation Hap1 and Hap2. But it is not in the configure file. If I only input the reference, it will have the following error: Start SV Simulation... 100%cat: /home/project11/Other_simulator/Sim-it/Long_reads_Test_my_HAP1.fasta: No such file or directory cat: /home/project11/Other_simulator/Sim-it/Long_reads_Test_my_HAP2.fasta: No such file or directory What should I do ?

[JEstabrook]

I'm encountering the same issue using the hg38 reference and the example_nstd152.vcf.

[ndierckx]

Sorry for the late reply, was very busy.

Could both of you share the log file, than I can see what the issue is, because you only need one reference, both haplotype files should be made by SIm-it.

[zixuanxie]

I'm also having the same issue, this is my log file:

---------------------------------CONFIG INPUT-----------------------------------

Input parameters from the configuration file: Verify if everything is correct

Project:

Project name = Test Reference = /hpcdata1/home/zxxie/DBs/hg38/bwa_index/hg38.fa Replace ambiguous nts(N) = Max threads = 15

Structural variation:

VCF input = Foreign sequences =

Deletions = 0 Length (bp) = 30-150000

Insertions = 0 Length (bp) = 30-100000

Tandem duplications = 0 Length (bp) = 50-10000 Copies = 1-20

Inversions = 0 Length (bp) = 150-1300000

Complex substitutions = 0 Length (bp) = 30-100000

Inverted duplications = 0 Length (bp) = 150-350000

Heterozygosity = no

Long Read simulation:

Sequencing depth = 0 Median length = 25000 Length range = 500-150000 Accuracy = 88 Error profile = error_profile_ONT.txt

---

Reference sequence

Contigs : 455 Reference Length : 3209286106 bp