Hi all, I have found a similar issue like https://github.com/nf-core/rnaseq/issues/694 in the nf-core/rnaseq pipeline, with:

The GTF file might be corrupted!
Stop at line : NC_011033.1    RefSeq  transcript  11024   315294  .   ?   .   gene_id "OrsajM_p01"; transcript_id "unassigned_transcript_653"; db_xref "GeneID:6450162"; exception "trans-splicing, RNA editing"; gbkey "mRNA"; gene "nad1"; locus_tag "OrsajM_p01"; transcript_biotype "mRNA";
Error Message: Strand is neither '+' nor '-'!"

The GTF is not corrupted however, directly downloaded from NCBI genome database. The reason for this seems to be very weird splicing in the Rice reference genome, where some CDS are on positive, and other on a negative strand, which means that the whole transcript doesn't have a single strand that it lies on, hence

?

. The offending part is this contig: https://www.ncbi.nlm.nih.gov/nuccore/NC_011033.1/ And here is a relevant sample from the GTF:

NC_011033.1	RefSeq	gene	11024	11409	.	+	.
NC_011033.1	RefSeq	gene	239890	315294	.	+	.
NC_011033.1	RefSeq	transcript	11024	315294	.	?	.
NC_011033.1	RefSeq	exon	11024	11409	.	+	.
NC_011033.1	RefSeq	exon	241499	241580	.	-	.
NC_011033.1	RefSeq	exon	239890	240081	.	-	.
NC_011033.1	RefSeq	exon	251354	251412	.	-	.
NC_011033.1	RefSeq	exon	315036	315294	.	-	.
NC_011033.1	RefSeq	CDS	11024	11409	.	+	0
NC_011033.1	RefSeq	CDS	241499	241580	.	-	1
NC_011033.1	RefSeq	CDS	239890	240081	.	-	0
NC_011033.1	RefSeq	CDS	251354	251412	.	-	0
NC_011033.1	RefSeq	CDS	315036	315291	.	-	1
NC_011033.1	RefSeq	start_codon	11024	11026	.	+	0
NC_011033.1	RefSeq	stop_codon	315036	315038	.	-	0

I have removed the offending genes from the GTF and so far we are chugging along. I have also checked the GTF2.2 specification and it doesn't mention

?

being an allowed symbol in the strand field. I have also reported this to the RSEM github repo, but the repo doesn't look very active: https://github.com/deweylab/RSEM/issues/220