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Old 08-03-2016, 12:30 PM   #1
ronaldrcutler
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Location: Virginia

Join Date: May 2016
Posts: 80
Default SSPACE library file

Hello all,

I have been trying to use SSPACE for scaffolding contigs in a de novo assembly, but can't seem to get the library file right. Here is the terminal command and Error:
Code:
perl /Users/confocal/Downloads/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl -l /Volumes/cachannel/RNA_SEQ/Reference_Genomes/Rhoddococcus_Build/SSPACE/library_file.txt -s /Volumes/cachannel/RNA_SEQ/Reference_Genomes/Rhoddococcus_Build/spades_super/Second_run/Spades_super_raw_contigs.fasta -T 8 -p 1
ERROR: Invalid (-l) library file /Volumes/cachannel/RNA_SEQ/Reference_Genomes/Rhoddococcus_Build/SSPACE/library_file.txt ...Exiting.
Here is the library file:
Code:
lib1 bowtie Erythropolis-gDNA_S1_L001_R1_001_val_1.fastq Erythropolis-gDNA_S1_L001_R2_001_val_2.fastq 399 0.25 FR
Any help with this? Thanks.
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