JunctionException using portcullis junc

[cc-prolix]

Hello,

I want to use portcullis in connection with Mikado.

I have created BAM files with HISAT2 (RNA-seq reads mapped to a reference genome) and indexing & sorting with samtools (samtools sort & samtools index). Portcullis prepare seems to work for me but when using "portcullis junc" I receive the following Error:

terminal input: portcullis prep GCA_001708085.1_ASM170808v1_genomic.fna SAMN07189663.bam portcullis junc portcullis_prep/

Error:

[fai_build_core] ignoring duplicate sequence "" at byte offset 94269314083394

• CP014708.1 [fai_fetch_seq] The sequence "CP014708.1" not found [fai_fetch_seq] The sequence "CP014708.1" not found terminate called after throwing an instance of 'boost::wrapexcept' what(): std::exception

I have also attached the whole output from portullis prep & portcullis junc if needed:

I thought this might be due to unmapped reads in the BAM file and extracted only mapped reads with samtools but received the same Error again.

Have you seen this before? Thanks for the help and please just tell me if you need more Info...

portcullis_aborted.txt

[cc-prolix]

I solved this problem. It looks like the BAM files were corrupted. Thanks