LTRHarvest - Ninja parameter

[Yiguan]

Hi,

I got the error message while running the LTR part:

LTR Structural Analysis
=======================
Running LtrHarvest...     : 00:59:53 (hh:mm:ss) Elapsed Time
Running Ltr_retriever...  : 00:30:01 (hh:mm:ss) Elapsed Time
Aligning instances...     : 02:04:53 (hh:mm:ss) Elapsed Time
Clustering...sh: line 1: 82011 Aborted                 /data/home/ywang120/NINJA-0.95-cluster_only/NINJA/Ninja --in /data/home/ywang120/myData/bbsrc2/idata/input_dat/ref_te/dana_te/test/RM_275793.ThuMay251441572023/LTR_171113.FriMay260636492023/mafft-alignment.fa --out /data/home/ywang120/myData/bbsrc2/idata/input_dat/ref_te/dana_te/test/RM_275793.ThuMay251441572023/LTR_171113.FriMay260636492023/NINJA_171113.FriMay261011362023/cluster.dat --out_type c --corr_type m --cluster_cutoff 0.2 --threads 20 > /data/home/ywang120/myData/bbsrc2/idata/input_dat/ref_te/dana_te/test/RM_275793.ThuMay251441572023/LTR_171113.FriMay260636492023/NINJA_171113.FriMay261011362023/Ninja.log 2>&1
LTRPipeline: Error - could not cluster MAFFT results.
             : 00:00:00 (hh:mm:ss) Elapsed Time
LTRPipeline : Error - could not open /data/home/ywang120/myData/bbsrc2/idata/input_dat/ref_te/dana_te/test/RM_275793.ThuMay251441572023/LTR_171113.FriMay260636492023/clusters.dat! at /data/home/ywang120/RepeatModeler-2.0.3/LTRPipeline line 333.
LTRPipeline Time: 03:34:51 (hh:mm:ss) Elapsed Time

Before I am trying to figure the error, I am confused about the Ninja parameters. The above log seems running with --out_type c --corr_type m --cluster_cutoff 0.2, but if I run Ninja --help, I don't see option 'c' for --out_type and 'm' for --corr_type , and there is no argment for --cluster_cutoff

$/data/home/ywang120/NINJA-0.95-cluster_only/NINJA/Ninja --help
Arguments:
--help (or -h) to display this help
--in (or -i) filename
--out (or -o) filename
--method (or -m)  [inmem | extmem] (default inmem)
--in_type type [a | d] (default a)
--out_type type [t | d] (default t)
--corr_type type [n | j | k | s]
--threads (or -T) num_threads
For more information, check the README file.

Thanks in advance!

[rmhubley]

You have the wrong version of NINJA. You named the directory "NINJA-0.95-cluster_only" but you have the standard version of the tool. When I run ./Ninja --help I get:

./Ninja --help
Ninja - Version 0.95-cluster_only

  ./Ninja --in file.fa --out file.out

Arguments: 
--help (or -h) to display this help
--in (or -i) filename
--out (or -o) filename
--in_type type [a | d] (default a)
--out_type type [d | c] (default c)
--corr_type type [n | j | k | s | m]
--cluster_cutoff dist_cutoff (default 0.03)
--threads (or -T) num_threads
--version (or -v) print the software version
For more information, check the README file.

When you download Ninja be sure to use this distribution: https://github.com/TravisWheelerLab/NINJA/releases/tag/0.95-cluster_only