which part should I modify?

[weifei888]

Firstly, My Bam file was sorted and indexed, the command "samtools view C0_3.sort.bam A01:16818-19507 " showed that there were a lot of reads.

Secondly,I modified the gff file, shown as:

A01 EVM gene 1913 2559 . - . ID=GH_A01G0001;
A01 EVM mRNA 1913 2559 . - . ID=GH_A01G0001;Parent=GH_A01G0001;
A01 EVM exon 2491 2559 . - . ID=exon:GH_A01G0001:1;Parent=GH_A01G0001;
A01 EVM CDS 2491 2559 . - 0 ID=CDS:GH_A01G0001:1;Parent=GH_A01G0001;
A01 EVM exon 2255 2365 . - . ID=exon:GH_A01G0001:2;Parent=GH_A01G0001;
A01 EVM CDS 2255 2365 . - 0 ID=CDS:GH_A01G0001:2;Parent=GH_A01G0001;
A01 EVM exon 1913 2134 . - . ID=exon:GH_A01G0001:3;Parent=GH_A01G0001;
A01 EVM CDS 1913 2134 . - 0 ID=CDS:GH_A01G0001:3;Parent=GH_A01G0001;

The gff was indexed by code "index_gff --index tm-1.gff tm-1"

And I ran:
miso --run tm-1 C0_3.sort.bam --output-dir C0_3 --read-len 150 --paired-end 250 15 --settings-filename miso_settings.txt

Then many directions were generated, however there was no result in each chromosome direction

I checked the log in batch-logs, there were some read, shown as:

Only 5 reads in gene, skipping (needed >= 20 reads)
Computing Psi for 1 genes...

• GH_D13G0036
• GFF filename: /mnt/f/MISO/tm-1_1/chrD13/GH_D13G0036.pickle
• BAM: /mnt/f/spladder/C0_3.sort.bam
• Outputting to: /mnt/f/MISO/C0_3_1
• Paired-end mode: (250.0, 15.0)
  Loading BAM filename from: /mnt/f/spladder/C0_3.sort.bam
  Filtered out 30 read pairs that were on same strand.
  Filtered out 29 reads that had no paired mate.
• Total read pairs: 516
  No. reads discarded due to strand violation: 0
  516 raw reads in event

So I am wondering if it is possible that you can show me which part should I to modify?