Li Fang

It seems that there are issues with your reference genome, because minimap2 reported the following: ``` loaded/built the index for 0 target sequence(s) distinct minimizers: 0 (-nan% are singletons); average...

OK. There will be a `run_minimap2.sample_name.sh` script in the `2_aligned_bam` folder. Could you please run it line-by-line and see what's happening.

minimap2 is not found. Please run it in the conda environment of nextsv.

There are two issues: 1) the memory is not enough as samtools reported `couldn't allocate memory for bam_mem`. 2) there is no valid sequence in your reference fasta file as...

You can reduce the `--threads` to 2 (the current value is 8) which might save some memory. It's best you can run it in a machine with at least 16G...

The first 20 lines are correct. I know this might be a modified reference genome. How about using the original reference genome to test the pipeline? If possible, you may...

Hello, Could you please show me: 1) the size of bam file in the `2_aligned_bam` folder 2) the shell scripts in `2_aligned_bam` and `3_SV_calls` Thanks! Li

The file sizes look correct. Could you please run the two shell scripts manually and see if any errors are reported? Thanks, Li

It looks like `minimap2` ran out of memory. Could you please run the following command and see what happened? `minimap2 --MD -t 2 -ax map-ont -N 10 /u/home/s/seichang/nextsv_input/chr19_new.fa /u/project/zarlab/seichang/nextsv/nextsv_output/1_clean_reads/sample_name.clean.fastq.gz /u/project/zarlab/seichang/nextsv/nextsv_output/1_clean_reads/sample_name.clean.fasta.gz...

Please run it in the conda environment of nextsv.