I aligned many fastq files with HISAT2 to grch38.  This proceeded without problems.

But in the next step with StringTie, which I am trying to find novel transcripts and their counts with the Gencode27 GTF:

    stringtie Donor1_IL2OKT3ZA.HISAT2.sort.bam -G /illumina/runs/RNASeq/Gencode27/gencode.v27.annotation.gtf -A try.tab -p 4 > stringtie.out 2> stringtie.err

However, I get an error

    WARNING: no reference transcripts were found for the genomic sequences where reads were mapped!
    Please make sure the -G annotation file uses the same naming convention for the genome sequences.

Why doesn't Stringtie recognize Gencode annotation? Do I have to do something to the gencode data?

Update: STAR works with this stringtie, but HISAT2 output doesn't.  Strange.

stringtie's output from `cut -f 3 try.tab | sort | uniq`

looks like

    703404669@ssxfisctimga004:~/RNASeq_benchmark/GSE96075/HISAT2$ cut -f 3 try.tab | sort | uniq
    1
    10
    11
    12
    13
    14
    15
    16
    17
    18
    19
    2
    20
    21
    22
    3
    4
    5
    6
    7
    8
    9
    GL000008.2
    GL000009.2
    GL000194.1
    GL000205.2
    GL000214.1
    GL000218.1
    GL000219.1
    GL000220.1
    GL000221.1
    GL000224.1
    KI270442.1
    KI270706.1
    KI270711.1
    KI270713.1
    KI270721.1
    KI270733.1
    KI270734.1
    KI270742.1
    KI270744.1
    KI270745.1
    MT
    Reference
    X
    Y
    chr1
    chr10
    chr11
    chr12
    chr13
    chr14
    chr15
    chr16
    chr17
    chr18
    chr19
    chr2
    chr20
    chr21
    chr22
    chr3
    chr4
    chr5
    chr6
    chr7
    chr8
    chr9
    chrM
    chrX
    chrY

UPDATE: I have found several other instances of this error, but no one ever addressed how to solve this:

https://github.com/gpertea/stringtie/issues/113

https://www.biostars.org/p/247954/

StringTie gave you an advice there, did you follow up on it?

>Please make sure the -G annotation file uses the same naming convention for the genome sequences.

In case you don't understand that message: it's about the chromosome names. The Gencode annotation uses chromosome names like *chr1*, *chr2* ,*chr3*,... while the grch38 alignments have *1*,*2*,*3*,.. instead. Hence that WARNING message.
Sure for you it might be obvious that "1" is the same as "chr1". But StringTie is made to work on any assembly/genome data, not just the human genome and it's not going to second guess your use of mismatching chromosome names like this..
I would suggest to use the UCSC hg38 genome instead -- or, if you don't want to re-run hisat2 again, find an annotation which uses the 1,2,3.. naming convention for the chromosomes.. or find a *reliable* way to convert the Gencode genomic sequence names to the grch38 naming convention.. This might be as simple as removing the "chr" prefix for the chromosome names -- but this might only work for the main chromosome sequences, the naming convention for the additional/alternate contigs might be different. 