IsoEM trying to run quantification but just prints out manual

Question

[mar77]

I'm trying to run IsoEM2 for the quantification of my RNA-seq experiment using the command:

     isoem2 [--GTF Homo_sapiens.GRCh38.99.chr.gtf]* [--auto-fragment-distrib]* SAMPLE.sam

as per their manual, but then the output I get is just:

isoem v 2.0.0
Usage: isoem [global options]* [library options]* <aligned_reads.sam>
Or: at <aligned_reads.sam> | isoem2 [global options]* [library options]*
Mandatory global options:
------------------------
-G, --GTF <GTF file>                    Known genes and isoforms in GTF format
Mandatory library options: either -a or both -m and -d must be present:
-------------------------
-m, --fragment-mean <Double>            Fragment length mean
-d, --fragment-std-dev <Double>         Fragment length standard deviation
-a, --auto-fragment-distrib             Automatically detect fragment length
                                          distribution from uniquely mapping
                                          paired reads (DOES NOT WORK FOR
                                          SINGLE READS)
Optional global options:
-----------------------
-c, --gene-clusters <Cluster file>      Override isoform to gene mapping
                                          defined in the GTF file with a
                                          mapping taken from the given file.
                                          The format of each line in the file
                                          is "isoform   gene"
-g <genome fasta file>                  Genome reference sequence (needed by
                                          some library options)
-b                                      Perform hexamer bias correction
-h, --help                              Show help
-r <Repeats GTF>                        Drop alignments falling within
                                          annotated repeats
Optional library options:
------------------------
-s, --directional                       Dataset obtained by directed RNA-Seq
                                          (the strand of each read is
                                          deterministically chosen: for single
                                          reads, the read always comes from
                                          the coding strand; for paired reads,
                                          the first read always comes from the
                                          coding strand, the second from the
                                          opposite strand)
--antisense                             Directional sequencing but the reads
                                          come from the antisense
--mate-pairs                            Paired reads come from the same strand
                                          (as opposed to the default behavior
                                          where the two reads in a pair are
                                          assumed to come from opposite
                                          strands)
--max-mismatches <Integer>              Maximum number of mismatched allowed
                                          for a read. This requires the genome
                                          sequence to be specified (see -g).
-q, --quality-scores                    Weigh the reads based on their quality
                                          scores. This requires the genome
                                          sequence to be specified (see -g).
--repeat-threshold <nbases>             Drop all reads that have more than
                                          this many bases inside annotated
                                          repeats. Default: 20.
--polyA <nbases>                        Reads have been generated from mRNAs
                                          with polyA tails of approximately
                                          the given number of bases
-o <file prefix>                        Output files prefix. It can include
                                          path. Default: same as sam file name
-O <directory prefix>                   Output directory prefix. If read
                                          alignments are read from stdin,
                                          the default value is stdinSample
-C <confidence interval (%)>            Compute expression of genes/isoforms
                                          with specified confidence intervals.
                                          Provide an integer (default: 95,
                                          bootstraps: 200)
--endseq                                Disable length normalization for data
                                          generated using 5' or 3' end-sequen-
                                          cing protocols, which generate a
                                          single fragment per cDNA molecule

It basically just prints out the manual, which does say to use isoem rather than isoem2 as the command, but when I have tried that it says

isoem: command not found

Does anyone have any idea where I might be going wrong and how to fix it?

[h.mon]

Is this the literal command you are running:

     isoem2 [--GTF Homo_sapiens.GRCh38.99.chr.gtf]* [--auto-fragment-distrib]* SAMPLE.sam

Or are you running:

     isoem2 --GTF Homo_sapiens.GRCh38.99.chr.gtf --auto-fragment-distrib SAMPLE.sam