Error: cannot find file 'stringtieout/ film_01.transcripts.gtf' and assemblies.txt does not look like GFF!

Question

[ccelispuga]

Hello ALL! Hope you are having a great new years so far!

I am back again with a question & would be delighted if I can have some help or suggestions (:

I am trying to merge a transcript but it is giving me a few errors. First I want to say that I HAVE tried a few times before posting to this website

1) tried deleting all uploaded codes/software then I re-installed all programs back on using terminal. The codes included the following:

• Hisat2 https://anaconda.org/bioconda/hisat2
• samtools https://anaconda.org/bioconda/samtools
• stringtie https://anaconda.org/bioconda/stringtie
• gffcompare https://anaconda.org/bioconda/gffcompare

2) The professor I am taking the class with provided a transcript for us to follow. I followed it to the T, w/o using any paths unless instructed. That codes is:

stringtie --merge -G paeruginosa.gff -o stringtie_merged.gtf assemblies.txt

3) Unfortunately it gives me 2 error msg, which are

Error: cannot find file 'stringtieout/ film_01.transcripts.gtf' and assemblies.txt does not look like GFF!

Any suggestions on how to fix this?

Thank in advance (:

[cpad0112]

As the error says, film_01.transcripts.gtf file either doesn't exist or placed elsewhere. Please check, if directory stringtieout exists or not. If it exists, look for the file. If gtf file doesn't exist, check the output (including error log) of previous commands. Please also check if the file exists, but not located in stringtieout directory.