assembly_improvement

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Intermediate file not found?

1

Dear @andrewjpage I've been trying, for a couple of days already, to properly install and run your assembly improvment pipeline. After installing all dependencies highlighted by `cpanm -f Bio::AssemblyImprovement` and...

joanmarticarreras

Could not read file (reference file) error

2

Hi @andrewjpage I ran assembly improvement against a spades assembly and a virus reference sequence provided on the command line and I get this error. I decided to just run...

george-githinji

Mummer error

1

ERROR: mummer and/or mgaps returned non-zero ERROR: Could not parse delta file, nucmer.delta Hi, I am getting this error while running ABACAS with the following params. $ perl abacas.1.3.1.pl -b...

koushik1989

Trying to use SSpace-Long Read

1

I have pre-assembled contigs from Canu. When I run the script: It gives me an error: Please insert a file with contig sequences. You've inserted '/SSPACE/SSPACE-LongRead_v1-1/runs/data/contigs.fasta' which either does not...

subnandakumar

Running abacas works fine when reference is in subfolder. But tblastx gives following error: ``` This may take several minutes ... [formatdb] ERROR: Could not open reference.fasta ERROR: Could not...

ghost

Tested using current version of SSPACE (SSPACE-STANDARD-3.0_linux-x86_64) as described in issue #67. Hopefully this is usable/mergeable as-is, but let me know if there are questions/concerns. I wouldn't want to accidentally...

coffeetocode

I have been using AssemblyImprover following VelvetOptimizer for 36 bacterial genomes. For the majority of the genomes, I generated the expected output files: contigs.fa.scaffolded.filtered contigs.fa.scaffolded.gapfilled.filtered scaffolds.scaffolded.gapfilled.length_filtered.fa scaffolds.scaffolded.gapfilled.length_filtered.sorted.fa But for a...

KrystalTW

It looks like maybe the expected input to SSPACE has changed since assembly_improvement was originally released. Running against the latest SSPACE (SSPACE-STANDARD-3.0_linux-x86_64) produces errors like: ``` ERROR: Invalid aligner in...

coffeetocode