Question: abundance_estimates_to_matrix.pl error while processing kallisto output
0
gravatar for Shahzad
10 weeks ago by
Shahzad10
Pakistan
Shahzad10 wrote:

Dear All please help me to solve this error.

perl abundance_estimates_to_matrix.pl --est_method kallisto --name_sample_by_basedir 1rc/1rc.tsv 2rc/2rc.tsv 3rc/3rc.tsv 1rt/1rt.tsv 2rt/2rt.tsv 3rT/3rt.tsv 1sc/1sc.tsv 2sc/2sc.tsv 3sc/3sc.tsv 1st/1st.tsv 2ST/2st.tsv 3st/3st.tsv --out_prefix guided-matrix --gene_trans_map none
-reading file: 1rc/1rc.tsv
-reading file: 2rc/2rc.tsv
-reading file: 3rc/3rc.tsv
-reading file: 1rt/1rt.tsv
-reading file: 2rt/2rt.tsv
-reading file: 3rT/3rt.tsv
-reading file: 1sc/1sc.tsv
-reading file: 2sc/2sc.tsv
-reading file: 3sc/3sc.tsv
-reading file: 1st/1st.tsv
-reading file: 2ST/2st.tsv
-reading file: 3st/3st.tsv


* Outputting combined matrix.

/home/ubuntu/Desktop/deg/support_scripts/run_TMM_scale_matrix.pl --matrix guided-matrix.isoform.TPM.not_cross_norm > guided-matrix.isoform.TMM.EXPR.matrixsh: 1: /home/ubuntu/Desktop/deg/support_scripts/run_TMM_scale_matrix.pl: not found
Error, CMD: /home/ubuntu/Desktop/deg/support_scripts/run_TMM_scale_matrix.pl --matrix guided-matrix.isoform.TPM.not_cross_norm > guided-matrix.isoform.TMM.EXPR.matrix died with ret 32512 at bundance_estimates_to_matrix.pl line 372.
ADD COMMENTlink modified 7 weeks ago by Biostar ♦♦ 20 • written 10 weeks ago by Shahzad10
/home/ubuntu/Desktop/deg/support_scripts/run_TMM_scale_matrix.pl: not found

This script is not present at a location where this tool expects it.

ADD REPLYlink written 10 weeks ago by ATpoint24k

is there any link to this file "run_TMM_scale_matrix.pl" . i am unable to find it in trinity pkg files

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Shahzad10

Here is the default path of run_TMM_scale_matrix.pl

trinityrnaseq/util/support_scripts/run_TMM_scale_matrix.pl

trinityrnaseq

ADD REPLYlink written 7 weeks ago by prince2612199130
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