When i run Trinity to get the transcripts abundances,i get the error like this,and i donot know what is wrong, below are the commonds and followings.
"../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir RSEM_outdir"
WARNING - appears that another process has started the rsem-prep step... proceeding with caution.
CMD: touch /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.RSEM.rsem.prepped.started
CMD: rsem-prepare-reference --transcript-to-gene-map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.gene_trans_map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.RSEM
rsem-synthesis-reference-transcripts /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.RSEM 0 1 /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.gene_trans_map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta
Mapping Info is not correct, cannot find TRINITY_DN44_c0_g1_i1's gene_id!
"rsem-synthesis-reference-transcripts /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.RSEM 0 1 /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.gene_trans_map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta" failed! Plase check if you provide correct parameters/options for the pipeline!
Error, cmd: rsem-prepare-reference --transcript-to-gene-map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.gene_trans_map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.RSEM died with ret: 65280 at ../../util/align_and_estimate_abundance.pl line 714.
"../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir RSEM_outdir"
WARNING - appears that another process has started the rsem-prep step... proceeding with caution.
CMD: touch /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.RSEM.rsem.prepped.started
CMD: rsem-prepare-reference --transcript-to-gene-map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.gene_trans_map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.RSEM
rsem-synthesis-reference-transcripts /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.RSEM 0 1 /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.gene_trans_map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta
Mapping Info is not correct, cannot find TRINITY_DN44_c0_g1_i1's gene_id!
"rsem-synthesis-reference-transcripts /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.RSEM 0 1 /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.gene_trans_map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta" failed! Plase check if you provide correct parameters/options for the pipeline!
Error, cmd: rsem-prepare-reference --transcript-to-gene-map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.gene_trans_map /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta /home/hupl/software/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.fasta.RSEM died with ret: 65280 at ../../util/align_and_estimate_abundance.pl line 714.
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