Bootstrap Confidence Tree Creation Mashtree Linux

Mashtree Bootstrap.pl command syntax to bootstrap confidence tree creation mashtree linux. Copyable examples, output expectations, and common mistakes.

More Mashtree Bootstrap.pl

Terminal

mashtree_bootstrap.pl --reps <100> --numcpus <12> <*.fastq.gz> -- --min-depth <0> > <mashtree.bootstrap.dnd>

mashtree_bootstrap.pl --reps <100> --numcpus <12> <*.fastq.gz> -- --min-depth <0> > <mashtree.bootstrap.dnd>

#!/bin/bash

# Bootstrap Confidence Tree Creation Mashtree Linux
mashtree_bootstrap.pl --reps {{100}} --numcpus {{12}} {{*.fastq.gz}} -- --min-depth {{0}} > {{mashtree.bootstrap.dnd}}

Command Result

What happens when it runs

Shell behavior

Primary Effect

Writes to file. The command sends content into the output file instead of printing the final result to the terminal.

Terminal Expectation

A successful run is usually quiet. Verify the destination file after execution rather than expecting visible stdout.

Troubleshooting

Common pitfalls

One of the input files does not exist

Solution: Check each input path before running the command.

The destination file or directory is not writable

Solution: Verify write permissions on the target path and parent directory.

Shell redirection points to the wrong file

Solution: Double-check the output path before executing, especially when overwriting with >.

Command Breakdown

What each part is doing

mashtree_bootstrap.pl: Base Command; The executable that performs this operation. Here it runs Mashtree Bootstrap.pl before the shell applies any redirect operators.
<100>: 100; The value supplied for 100.
<12>: 12; The value supplied for 12.
<*.fastq.gz>: *.fastq.gz; The value supplied for *.fastq.gz.
<0>: 0; The value supplied for 0.
--reps: Command Option; Tool-specific option used by this command invocation.
--numcpus: Command Option; Tool-specific option used by this command invocation.
--: Command Option; Tool-specific option used by this command invocation.
--min-depth: Command Option; Tool-specific option used by this command invocation.
>: Output Redirection; Writes the command output to the output file, replacing any existing content.
<mashtree.bootstrap.dnd>: Destination Path; The file that receives the final written output.