WARNING: The graph has an edge between non-existant node(s) about aeron

[ddurai]

Dear Lane Zao,
Thank you for trying our software and pointing out the issue. In cases where two nodes arise from the same genomic region (with the same genomic coordinates), we keep only one node and remove the other. But I realized the graph builder is still building an edge between the two nodes. But this would not affect the alignment, quantification and gene-fusion detection process

[ddurai]

Dear Lane Zao,
Can you please point me to the input fastq file you are using and also can you attach the log file here

[lane-zhao]

The fastq file I used is from Nanopore cDNA longreads sequenece about human tissue.
The .gfa file is used GraphBuilder.py to generated.
I supposed their have something wrong in GraphBuilder.py .

Aligner.log

[SchulzLab]

Dear lane-zhao,
can you please give more information on the annotation file you use and the command for building the graph file.

Thanks,
Marcel

[lane-zhao]

The genome and gtf file was download from ensemble version: release-94 Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa and corresponding gtf file.
The command I used is >python GraphBuilder.py -e Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa -g hg38.gtf -o hg38.gfa
The format of the gtf file and hg38.gfa which I generated are in the attach.txt

attach.txt

[ddurai]

Dear Lane Zao
The format of the genome file you used was slightly different than the format which we used for generating the graph and testing our codes. This difference was not accounted for in the previous version of the GraphBuilder script. But I assure you that this bug does not change the results which we have reported in the manuscript.
I have fixed the bug and uploaded the new version. Can you please try generating the graph file again with the new version and test the aligner. I apologize for the inconvenience caused to you

[lane-zhao]

The updated script is working well. But then I have a new question, in file Snakefile_fusion， line 61: transcriptaln = "output/aln_{transcripts}_{graph}_full_length.gam", any steps to generated this file ?
The error is : MissingInputException in line 59 of Snakefile_fusion: `input files for rule pair_assignments. I supposed this step was missed.