RSEM-calculate-expression error

[SisiChen16]

Hi,
I've got some issues with RSEM-calculate-expression, here's the code I used:

RSEM-1.3.3/rsem-calculate-expression -p 8 --paired-end --bowtie2 --bowtie2-path /Users/chensisi/Documents/miniconda3/envs/RSEM/bin --append-names --output-genome-bam Documents/pair1.fq Documents/pair2.fq /RSEM_tutorial/human_rsem RSEM_tutorial/RSEM_test

The error message is shown below:

readline() on closed filehandle INPUT at RSEM-1.3.3/rsem-calculate-expression line 361.
Use of uninitialized value $line in scalar chomp at RSEM-1.3.3/rsem-calculate-expression line 361.
Use of uninitialized value $line in split at RSEM-1.3.3/rsem-calculate-expression line 363.
Use of uninitialized value $type in numeric ne (!=) at RSEM-1.3.3/rsem-calculate-expression line 364.
/Users/chensisi/Documents/miniconda3/envs/RSEM/bin/bowtie2 -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 8 -k 200 -x /RSEM_tutorial/human_rsem -1 Documents/pair1.fq -2 Documents/pair2.fq 2> RSEM_tutorial/RSEM_test.log | samtools view -b -o RSEM_tutorial/RSEM_test.temp/RSEM_test.bam -

rsem-parse-alignments /RSEM_tutorial/human_rsem RSEM_tutorial/RSEM_test.temp/RSEM_test RSEM_tutorial/RSEM_test.stat/RSEM_test RSEM_tutorial/RSEM_test.temp/RSEM_test.bam 3 -tag XM
Cannot open /RSEM_tutorial/human_rsem.grp! It may not exist.

"rsem-parse-alignments /RSEM_tutorial/human_rsem RSEM_tutorial/RSEM_test.temp/RSEM_test RSEM_tutorial/RSEM_test.stat/RSEM_test RSEM_tutorial/RSEM_test.temp/RSEM_test.bam 3 -tag XM" failed! Plase check if you provide correct parameters/options for the pipeline!

It seems that the "human_rsem.grp" file is not exist, but I've already done the "rsem-prepare-reference" step to generate the "grp" file, here's the code I used:

RSEM-1.3.3/rsem-prepare-reference --gtf Ref/Homo_sapiens.GRCh38.105.chr.gtf --bowtie2 --bowtie2-path /Users/chensisi/Documents/miniconda3/envs/RSEM/bin Ref/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa RSEM_tutorial/human_rsem

As I opened the "human_rsem.grp" file on command, it shows only numbers in it (as below), is there any issues with my procedure or something wrong with the package? Could you help me troubleshoot this?

1
6
8
24
29
38
45
51
54
68
70
...

Best wishes,
Sisi