I tried running the align_and_estimate_abundance.pl (Trinity-RSEM pipeline) with the following:

align_and_estimate_abundance.pl --transcripts $TRANSCRIPTS \
        --seqType fq \
        --left read_L_1.fastq,read_L_2.fastq,read_L_3.fastq,\
               read_L_4.fastq,read_L_5.fastq,read_L_6.fastq \
        --right read_R_1.fastq,read_R_2.fastq,read_R_3.fastq,\
                read_R_4.fastq,read_R_5.fastq,read_R_6.fastq \
        --est_method RSEM \
        --aln_method bowtie \
        --trinity_mode \
        --prep_reference

But I got the following error:

WARNING - looks like the prep for /nfs/users/...bowtie was already started by another process. Proceeding with caution.
CMD: touch /nfs/users/...bowtie.started
CMD: bowtie-build /nfs/users/...bowtie
Warning: Empty input file
Error: No unambiguous stretches of characters in the input. Aborting...
Command: bowtie-build /nfs/users/...bowtie
Error, cmd: bowtie-build /nfs/users/...bowtie died with ret: 256 at /apps/trinity/trinity_2.0.6/util/align_and_estimate_abundance.pl line 653.
srun: error: cfb-smp1: task 0: Exited with exit code 2

The bowtie was already started by another process comment always comes up every time I try a revised script. Is it possible to "reset" this somehow?

I'm new to this and I can't identify the problem. Please help me make this work. Thank you in advance for your help!