Unable to find combined.gtf file

[bimbim1803]

Hi,
I'm trying to run FINDER for a Hawaiian Drosophila genome. However, I got this problem: " FileNotFoundError: [Errno 2] No such file or directory: '/storage/pricelab/ngoc/Finder-finder_v1.1.0/silvestris/assemblies_psiclass_modified/combined/combined.gtf'
Please let me know if you need any information from me. Thank you so much!

[bimbim1803]

An update on this issue:
When i go to combined.error file at this directory: /storage/pricelab/ngoc/Finder-finder_v1.1.0/silvestris/assemblies_psiclass_modified/combined, I got this message:
"[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Can not open /storage/pricelab/ngoc/Finder-finder_v1.1.0/test/alignments/sample1_for_psiclass.bam.
Terminated"

So I went to /storage/pricelab/ngoc/Finder-finder_v1.1.0/test/alignments and see that even though there is a file named sample1_for_psiclass.bam, it was empty without any content in it. Please see the attached files
sample1_round5_r.error.txt
combined.error.txt
. I'm not sure where to check for the error on that. Any guidance is appreciated! Thank you!

[sagnikbanerjee15]

Hello @bimbim1803,

Thank you for your patience on this matter and thanks for using finder. It seems like there is an issue with either olego mapping or merging of files. Could you please confirm that alignments are present for STAR?

Thank you,
Sagnik