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ssr2marker运行示例文件报错 #1

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ssr2marker运行示例文件报错#1
@xiaohaijie

Description

@xiaohaijie
xiaohaijie
opened on Mar 27, 2023

Hello! I download in accordance with the instructions to the linux system to run the error again, the error is as follows (with running process), I would like to ask where there is a problem? Thank you!

报错内容：ssr2marker

(py27) perl SSR2Marker.pl -f1 Hongyang_genome_v2.0.fa -f2 White_genome_v1.0.fasta

Beginning to check the dependent softwares needed in this program ...

The PERL software could be correctly called.

The BLASTN software could be correctly called.

The MAFFT software could be correctly called.

The PRIMER3_CORE software could be correctly called.

The RE-PCR software could be correctly called.

All dependent softwares could be correctly called here.

Preparing the working directory ...

The working directory is successfully built.

Beginning to identify the SSRs in the input files ...

Finishing the identification of SSRs.

Grabbing the SSR sequences as well as their upstream and downstream sequences ...

Building a new DB, current time: 03/22/2023 20:44:19

New DB name: /home/gaojie/duotai/temp/db/reference.fasta

New DB title: ./temp/db/reference.fasta

Sequence type: Nucleotide

Keep MBits: T

Maximum file size: 1000000000B

Adding sequences from FASTA; added 682673 sequences in 20.8117 seconds.

Beginning to identify single-copy SSRs ...

Finishing the identification of single-copy SSRs.

SSR, upstream and downstream sequences are obtained.

Beginning to identify the identical regions within upstream and downstream sequences, respectively ...

Finishing the identification of identical regions.

Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008

Whitehead Institute for Biomedical Research, Steve Rozen

(http://purl.com/STEVEROZEN/), Andreas Untergasser and Helen Skaletsky

All rights reserved.

This file is part of the primer3 suite and libraries.



The primer3 suite and libraries are free software;

you can redistribute them and/or modify them under the terms

of the GNU General Public License as published by the Free

Software Foundation; either version 2 of the License, or (at

your option) any later version.



This software is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.



You should have received a copy of the GNU General Public License

along with this software (file gpl-2.0.txt in the source

distribution); if not, write to the Free Software

Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS

"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT

LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR

A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT

OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,

SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT

LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,

DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY

THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

USAGE: primer3_core [-format_output] [-io_version=3|-io_version=4] [-p3_settings_file=<file_path>] [-strict_tags]

This is primer3 (primer3 release 2.0.0)

Input must be provided on standard input.

For example:

$ primer3_core < my_input_file

  • Adding ./temp/epcr/Hongyang_genome_v2.0.fasta

  • Adding ./temp/epcr/White_genome_v1.0.fasta

  • Adding File ./temp/epcr/Hongyang_genome_v2.0.famap

  • Adding Sequence Hongyang_genome_v2.0000001

  • Adding Sequence Hongyang_genome_v2.0000002

  • Adding Sequence Hongyang_genome_v2.0000003

  • Adding Sequence Hongyang_genome_v2.0000004

  • Adding Sequence Hongyang_genome_v2.0000005

  • Adding Sequence Hongyang_genome_v2.0000006

  • Adding Sequence Hongyang_genome_v2.0000007

  • Adding Sequence Hongyang_genome_v2.0000008

  • Adding Sequence Hongyang_genome_v2.0000009

  • Adding Sequence Hongyang_genome_v2.0000010

  • Adding Sequence Hongyang_genome_v2.0000011

  • Adding Sequence Hongyang_genome_v2.0000012

  • Adding Sequence Hongyang_genome_v2.0000013

  • Adding Sequence Hongyang_genome_v2.0000014

  • Adding Sequence Hongyang_genome_v2.0000015

  • Adding Sequence Hongyang_genome_v2.0000016

  • Adding Sequence Hongyang_genome_v2.0000017

  • Adding Sequence Hongyang_genome_v2.0000018

  • Adding Sequence Hongyang_genome_v2.0000019

  • Adding Sequence Hongyang_genome_v2.0000020

  • Adding Sequence Hongyang_genome_v2.0000021

  • Adding Sequence Hongyang_genome_v2.0000022

  • Adding Sequence Hongyang_genome_v2.0000023

  • Adding Sequence Hongyang_genome_v2.0000024

  • Adding Sequence Hongyang_genome_v2.0000025

  • Adding Sequence Hongyang_genome_v2.0000026

  • Adding Sequence Hongyang_genome_v2.0000027

  • Adding Sequence Hongyang_genome_v2.0000028

  • Adding Sequence Hongyang_genome_v2.0000029

  • Adding Sequence Hongyang_genome_v2.0000030

OKTotal number of sequences: 30

Number of hash entries: 196608

Average number of sequences per hash entry: 30

Maximal number of sequences per hash entry: 30

Null hash entries: 0

Total number of hits: 1812145010

Average number of hits per hash entry: 9217.05

Maximal number of hits per hash entry: 635498

  • Adding Sequence Hongyang_genome_v2.0000001

= Dumping

= Dumping OK

= Dumping

= Dumping OK

  • Adding Sequence Hongyang_genome_v2.0000002

  • Adding Sequence Hongyang_genome_v2.0000003

  • Adding Sequence Hongyang_genome_v2.0000004

= Dumping

= Dumping OK

  • Adding Sequence Hongyang_genome_v2.0000005

  • Adding Sequence Hongyang_genome_v2.0000006

  • Adding Sequence Hongyang_genome_v2.0000007

  • Adding Sequence Hongyang_genome_v2.0000008

= Dumping

= Dumping OK

  • Adding Sequence Hongyang_genome_v2.0000009

  • Adding Sequence Hongyang_genome_v2.0000010

  • Adding Sequence Hongyang_genome_v2.0000011

  • Adding Sequence Hongyang_genome_v2.0000012

= Dumping

= Dumping OK

  • Adding Sequence Hongyang_genome_v2.0000013

  • Adding Sequence Hongyang_genome_v2.0000014

  • Adding Sequence Hongyang_genome_v2.0000015

  • Adding Sequence Hongyang_genome_v2.0000016

= Dumping

= Dumping OK

  • Adding Sequence Hongyang_genome_v2.0000017

  • Adding Sequence Hongyang_genome_v2.0000018

  • Adding Sequence Hongyang_genome_v2.0000019

  • Adding Sequence Hongyang_genome_v2.0000020

  • Adding Sequence Hongyang_genome_v2.0000021

= Dumping

= Dumping OK

  • Adding Sequence Hongyang_genome_v2.0000022

  • Adding Sequence Hongyang_genome_v2.0000023

  • Adding Sequence Hongyang_genome_v2.0000024

  • Adding Sequence Hongyang_genome_v2.0000025

= Dumping

= Dumping OK

  • Adding Sequence Hongyang_genome_v2.0000026

  • Adding Sequence Hongyang_genome_v2.0000027

  • Adding Sequence Hongyang_genome_v2.0000028

  • Adding Sequence Hongyang_genome_v2.0000029

  • Adding Sequence Hongyang_genome_v2.0000030

= Dumping

= Dumping OK

= Dumping

= Dumping OK

  • Adding File ./temp/epcr/White_genome_v1.0.famap

  • Adding Sequence White_genome_v1.0000001

  • Adding Sequence White_genome_v1.0000002

  • Adding Sequence White_genome_v1.0000003

  • Adding Sequence White_genome_v1.0000004

  • Adding Sequence White_genome_v1.0000005

  • Adding Sequence White_genome_v1.0000006

  • Adding Sequence White_genome_v1.0000007

  • Adding Sequence White_genome_v1.0000008

  • Adding Sequence White_genome_v1.0000009

  • Adding Sequence White_genome_v1.0000010

  • Adding Sequence White_genome_v1.0000011

  • Adding Sequence White_genome_v1.0000012

  • Adding Sequence White_genome_v1.0000013

  • Adding Sequence White_genome_v1.0000014

  • Adding Sequence White_genome_v1.0000015

  • Adding Sequence White_genome_v1.0000016

  • Adding Sequence White_genome_v1.0000017

  • Adding Sequence White_genome_v1.0000018

  • Adding Sequence White_genome_v1.0000019

  • Adding Sequence White_genome_v1.0000020

  • Adding Sequence White_genome_v1.0000021

  • Adding Sequence White_genome_v1.0000022

  • Adding Sequence White_genome_v1.0000023

  • Adding Sequence White_genome_v1.0000024

  • Adding Sequence White_genome_v1.0000025

  • Adding Sequence White_genome_v1.0000026

  • Adding Sequence White_genome_v1.0000027

  • Adding Sequence White_genome_v1.0000028

  • Adding Sequence White_genome_v1.0000029

  • Adding Sequence White_genome_v1.0000030

OKTotal number of sequences: 30

Number of hash entries: 196608

Average number of sequences per hash entry: 30

Maximal number of sequences per hash entry: 30

Null hash entries: 0

Total number of hits: 2071004209

Average number of hits per hash entry: 10533.7

Maximal number of hits per hash entry: 763582

  • Adding Sequence White_genome_v1.0000001

  • Adding Sequence White_genome_v1.0000002

  • Adding Sequence White_genome_v1.0000003

= Dumping

= Dumping OK

  • Adding Sequence White_genome_v1.0000004

  • Adding Sequence White_genome_v1.0000005

  • Adding Sequence White_genome_v1.0000006

= Dumping

= Dumping OK

  • Adding Sequence White_genome_v1.0000007

  • Adding Sequence White_genome_v1.0000008

  • Adding Sequence White_genome_v1.0000009

= Dumping

= Dumping OK

  • Adding Sequence White_genome_v1.0000010

  • Adding Sequence White_genome_v1.0000011

  • Adding Sequence White_genome_v1.0000012

= Dumping

= Dumping OK

  • Adding Sequence White_genome_v1.0000013

  • Adding Sequence White_genome_v1.0000014

  • Adding Sequence White_genome_v1.0000015

= Dumping

= Dumping OK

  • Adding Sequence White_genome_v1.0000016

  • Adding Sequence White_genome_v1.0000017

= Dumping

= Dumping OK

  • Adding Sequence White_genome_v1.0000018

  • Adding Sequence White_genome_v1.0000019

  • Adding Sequence White_genome_v1.0000020

= Dumping

= Dumping OK

  • Adding Sequence White_genome_v1.0000021

  • Adding Sequence White_genome_v1.0000022

  • Adding Sequence White_genome_v1.0000023

= Dumping

= Dumping OK

  • Adding Sequence White_genome_v1.0000024

  • Adding Sequence White_genome_v1.0000025

  • Adding Sequence White_genome_v1.0000026

= Dumping

= Dumping OK

  • Adding Sequence White_genome_v1.0000027

  • Adding Sequence White_genome_v1.0000028

  • Adding Sequence White_genome_v1.0000029

= Dumping

= Dumping OK

  • Adding Sequence White_genome_v1.0000030

= Dumping

= Dumping OK

cp: 无法获取"./Running_SSR2Marker_20230322203146/primer_overall.txt" 的文件状态(stat): 没有那个文件或目录

cp: 无法获取"./Running_SSR2Marker_20230322203146/*.stat" 的文件状态(stat): 没有那个文件或目录

Error in SSR2Marker.pl: No such file or directory !

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