Hi, I am using the following script: /usr/local/src/Trinity/trinityrnaseq-v2.9.0/util/abundance_estimates_to_matrix.pl --est_method RSEM --out_prefix Hvansoes_final --gene_trans_map trinity_Haliclona.Trinity.fasta.gene_trans_map --name_sample_by_basedir MA6_1/RSEM.isoforms.results MA6_2/RSEM.isoforms.results MA6_3/RSEM.isoforms.results CO6_4/RSEM.isoforms.results CO6_6/RSEM.isoforms.results CO6_8/RSEM.isoforms.results DI3_10/RSEM.isoforms.results DI3_12/RSEM.isoforms.results DI3_12/RSEM.isoforms.results

and I get this error: -reading file: MA6_1/RSEM.isoforms.results -reading file: MA6_2/RSEM.isoforms.results -reading file: MA6_3/RSEM.isoforms.results -reading file: CO6_4/RSEM.isoforms.results -reading file: CO6_6/RSEM.isoforms.results -reading file: CO6_8/RSEM.isoforms.results -reading file: DI3_10/RSEM.isoforms.results -reading file: DI3_12/RSEM.isoforms.results -reading file: DI3_12/RSEM.isoforms.results

• Outputting combined matrix.

Error, the column headings: MA6_1 MA6_2 MA6_3 CO6_4 CO6_6 CO6_8 DI3_10 DI3_12 DI3_12 are not unique. Should you consider using the --name_sample_by_basedir parameter? at /usr/local/src/Trinity/trinityrnaseq-v2.9.0/util/abundance_estimates_to_matrix.pl line 247.

But I am already using the -name_sample_by_basedir parameter. What am I doing wrong? Can you help me please? Best, Ana