This is a test version of Biostars. For the public version, visit https://www.biostars.org.
SSPace | Search Pattern Terminated

Hello! this is my first time posting here.

I'm running a perl script but I keep on getting an error.

perl_script:

#!/usr/bin/perl 

perl ../SSPACE_Basic_v2.0.pl -l libraries.txt -s contigs_C3.fasta -x 1 -o 20 -k 5 -a 0.7 -m 30 -b C3_with_extensions

error:

Search pattern not terminated at ./sspace_script_C3_readable_v2.sh line 3.

How I could fix this? Thank you!

sspace
• 964 views • link
written by mercadomarkcyril28 • mercadomarkcyril28

The shebang (#!) line indicates that the code is perl code while you run shell code. Change it to #!/usr/bin/bash

• 0 views • link
written by Asaf Asaf

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • Bowtie-build error; -1 using SSPACE for scaffolding
    written by Kacper • Kacper
    I'm very new to bioinformatics and currently struggling. I used SPAdes to assemble a bacterial genome and attempted to scaffold using SSPACE. My command was: …
  • Gapfiller creates more mismatches than SSPACE. Why?
    written by karenclarom9 • karenclarom9
    Hi everyone! I chose SSPACE to form scaffolds and it seemed to work well. I obtained 20 mismatches (N's). But, when I tried to fill …
  • Help with Tophat2 run
    written by Neu • Neu
    Hi, I am getting the error as below when trying to run tophat2. Please help me to resolve this. command: tophat2 -o tophat_fusion --fusion-search --keep-fasta-order …
  • Parclip suite usage
    written by pandikannan4 • pandikannan4
    I am trying to use Parclip suite (Rockefeller university) for analysing my PAR-CLIP data. I can process my files upto the stage of collapsed fasta …
  • Bowtie run error
    written by mikemwanga6 • mikemwanga6
    I am running SSPACE after assembly of reads using SPADES. However SSPACE returns the following error. command: perl ~/my_scripts/SSPACE/SSPACE_Basic.pl -l libraries.txt -s contigs.fasta -k 5 …
  • Bowtie2 Build error in CygWin
    written by NGS-Newbie • NGS-Newbie
    Hi All I am trying to build bowtie2 on cygwin (Windows10). I tried to "make" it from the source file. 1) Even after installing Thread …
  • evigene pipeline failure: missing cdna_bestorf.pl
    written by lplough • lplough
    Hi I am trying out the evigene evidential gene pipeline http://arthropods.eugenes.org/EvidentialGene/ on some multi K-mer transcriptome assemblies. I have had a difficult time getting it …
  • SSPACE assembling Genome!
    written by fufuyou fufuyou
    Hi , I am assembling a genome using SSPACE. I met a problem as: perl /scratch/snyder/f/fu115/Genome_assembly/SSPACE/41SSPACE-STANDARD-3.0_linux-x86_64/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl -l libraries.txt -s contigs_abyss.fasta -k 5 -a 0.7 -x …
  • Any experience with scaffolding using SSPACE tool
    written by seta seta
    Hi all, I made de novo transcriptome assembly using about 300 millions PE reads (100bp from Illumina) with different k-mers. Several assembled transcriptome was merged …
  • -m is not work in vcf-compare option
    written by Anop Singh Ranawat • Anop Singh Ranawat
    `-m` is not work in vcf-compare option vcf-compare -m *.vcf.gz Missing argument in sprintf at /usr/local/bin/vcf-compare line 142. Invalid conversion in sprintf: "%\232" at /usr/local/bin/vcf-compare …