Count matrix error. abundance_estimates_to_matrix.pl Error
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Entering edit mode
6.5 years ago

Hi everyone,

I am trying to generate a count matrix using abundance_estimates_to_matrix.pl script in Trinity, but I keep running into the same error. I fed the script 36 RSEM.genes.results files:

perl /usr/local/bin/trinityrnaseq-2.0.6/util/abundance_estimates_to_matrix.pl --est_method RSEM --name_sample_by_basedir ~/aligning/final/R1_Samples/22/RSEM.genes.results ~/aligning/final/R1_Samples/29/RSEM.genes.results ~/aligning/final/R1_Samples/34/RSEM.genes.results ~/aligning/final/R1_Samples/39/RSEM.genes.results ~/aligning/final/R1_Samples/42/RSEM.genes.results ~/aligning/final/R1_Samples/49/RSEM.genes.results ~/aligning/final/R1_Samples/60/RSEM.genes.results ~/aligning/final/R1_Samples/6/RSEM.genes.results ~/aligning/final/R2_Samples/13/RSEM.genes.results ~/aligning/final/R2_Samples/18/RSEM.genes.results ~/aligning/final/R2_Samples/1/RSEM.genes.results ~/aligning/final/R2_Samples/33/RSEM.genes.results ~/aligning/final/R2_Samples/46/RSEM.genes.results ~/aligning/final/R2_Samples/57/RSEM.genes.results ~/aligning/final/R2_Samples/59/RSEM.genes.results ~/aligning/final/R2_Samples/5/RSEM.genes.results ~/aligning/final/R2_Samples/62/RSEM.genes.results ~/aligning/final/R3_Samples/14/RSEM.genes.results ~/aligning/final/R3_Samples/16/RSEM.genes.results ~/aligning/final/R3_Samples/20/RSEM.genes.results ~/aligning/final/R3_Samples/20/RSEM.genes.results ~/aligning/final/R3_Samples/31/RSEM.genes.results ~/aligning/final/R3_Samples/54/RSEM.genes.results ~/aligning/final/R4_Samples/14/RSEM.genes.results ~/aligning/final/R4_Samples/23/RSEM.genes.results ~/aligning/final/R4_Samples/25/RSEM.genes.results ~/aligning/final/R4_Samples/54/RSEM.genes.results ~/aligning/final/R4_Samples/54/RSEM.genes.results ~/aligning/final/R4_Samples/6/RSEM.genes.results ~/aligning/final/R4_Samples/9/RSEM.genes.results ~/aligning/final/R5_Samples/19/RSEM.genes.results ~/aligning/final/R5_Samples/28/RSEM.genes.results ~/aligning/final/R5_Samples/33/RSEM.genes.results ~/aligning/final/R5_Samples/4/RSEM.genes.results ~/aligning/final/R5_Samples/54/RSEM.genes.results ~/aligning/final/R5_Samples/8/RSEM.genes.results

Here is the error: Error, the column headings: 22 29 34 39 42 49 60 6 13 18 1 33 46 57 59 5 62 14 16 20 20 31 54 14 23 25 54 54 6 9 19 28 33 4 54 8 are not unique. Should you consider using the --name_sample_by_basedir parameter? at /usr/local/bin/trinityrnaseq-2.0.6/util/abundance_estimates_to_matrix.pl line 174.

I have added in the name sample by base directory parameter, so I am not sure how to fix this. Any help would be appreciated!

Thanks, Nikelle

trinity RNA-Seq count matrix DE • 1.6k views
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Entering edit mode
6.4 years ago

You're listing the same sample(s) twice e.g. ~/aligning/final/R3_Samples/20/RSEM.genes.results ~/aligning/final/R3_Samples/20/RSEM.genes.results

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