Tcoffee run finishes with empty results

Hi There

I was trying to run T-Coffee as a part of GeneSeqToFamily, it runs fine but generates empty results

I am pasting the job information at the bottom.

The same tool works fine on other Galaxy instance like Earlham Galaxy with same input and parameter.


Dataset Information

Number: 15
Name: T-Coffee on data 11 and data 4: fasta_aln
Created: Tue Jun 2 13:17:27 2020 (UTC)
Filesize: 0 bytes
Dbkey: ?
Format: fasta

Job Information

Galaxy Tool ID:
Galaxy Tool Version: 11.0.8_1
Tool Version:
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: 0
History Content API ID: 11ac94870d0bb33a33a75abedcb79829
Job API ID: d555908874dbb0b7
History API ID: 719b9d39b9c90925
UUID: c7e3c952-066d-426c-a610-68773300f855
Full Path: /data/dnb02/galaxy_db/files/020/507/dataset_20507420.dat

Tool Parameters

Input Parameter Value
Filter FASTA input? yes
FASTA sequences * 4: transeq on data 1
List of FASTA sequence IDs * 11: 0
Pairwise Structual Method Nothing selected.
Multiple Sequence Alignment Methods clustalw_msa
Pairwise Sequence Alignment Methods Nothing selected.
Output formats fasta_aln

Inheritance Chain

1 Like

I had the same problem using t coffee. I wish someone will reply to you.

1 Like

ping @bjoern.gruening @wm75

This is an issue in upstream T-Coffee MAX_N_PID should be 4194304 on 64bit machines · Issue #27 · cbcrg/tcoffee · GitHub , which I have worked around in Update t-coffee to by nsoranzo · Pull Request #25932 · bioconda/bioconda-recipes · GitHub for the conda package. I’ve started updating the t_coffee Galaxy tool to make use of this new package in Update t_coffee to version by nsoranzo · Pull Request #139 · TGAC/earlham-galaxytools · GitHub .