R featureCounts throws error over SAF format

Question

[1111111]

Hello,

I'm trying to run R featureCounts on SAM files with a SAF annotation file that looks like this:

Chr Start   End Strand  GeneID
NC_000067.6 3102016 3102125 +   LOC115487594
NC_000067.6 3102016 3102125 +   LOC115487594
NC_000067.6 3199733 3671948 -   Xkr4
NC_000067.6 3199733 3671948 -   Xkr4
NC_000067.6 3214482 3671498 -   Xkr4
NC_000067.6 3216022 3671348 -   Xkr4
NC_000067.6 3216022 3671348 -   Xkr4
NC_000067.6 3252734 3253236 +   Gm18956
NC_000067.6 3322816 3671948 -   Xkr4
........

The Chr values are accessions on purpose, since this is what appears in my SAM files and I read they should me the same.

I ran the following command:

> fc <- featureCounts(filenames, annot.ext ="./feature_table_intervals.tsv", isGTFAnnotationFile = FALSE)

And got the following output:

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 1.32.4

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 SAM file                                       ||
||                           S aged12h2002.fastq_1_40.trimmed_genome_-l_4 ... ||
||                                                                            ||
||              Annotation : feature_table_intervals.tsv (SAF)                ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : no                                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : not counted                                      ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file feature_table_intervals.tsv ...                       ||

Error: Line 1 contains a format error. The expected annotation format is SAF.
Error in featureCounts(filenames, annot.ext = "./feature_table_intervals.tsv",  : 
  No counts were generated.
>

Can anyone help me with what the problem is here? I generated the tsv file according to the SAF format definition I found here: https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts Ant idea what am I doing wrong? Thank you