Question: SSPACE file error
3
gravatar for susannehoward
4.2 years ago by
United States
susannehoward90 wrote:

I am trying to use SSPACE for scaffolding, but get stuck at the very first step: somehow SSPACE cannot read  my file or else I am not sure what leads to this error:

ERROR: Invalid file in library Lib1: ~/Desktop/RawSequences/Fastq/3kbFor_pair2.fastq -- fatal

It can't be the file itself, I am using bwa for the alignment step and doing the aligning step separately works just fine.

Anyone have any ideas??

 

alignment assembly • 2.3k views
ADD COMMENTlink modified 2.8 years ago by psthomas0 • written 4.2 years ago by susannehoward90

I found on the seqanswers a similar error: http://seqanswers.com/forums/archive/index.php/t-21493.html

But anyone reply/helped him. 

Although, him pointed out that maybe the formatation of the header may be the origin of the error, maybe smth that bwa ignores.

Dont helped much but, maybe is worth to check the headers.

Original post:

"04-11-2014, 06:07 AM

I am receiving an error when running SSPACE to get a scaffold for GAPfiller.
"ERROR: Invalid file in library Lib1: ~/scratch/bob/lotus/Illumina_3kb_1_R1.fastq -- fatal"

Below is what the head of my fastq file looks like and I don't see where there may be a formatting error. Has anyone else seen and fixed this error?

@DBRHHJN1:175:C011MACXX:3:1101:1149:1049 1:N:0:ATCACG
TCAGGGCATTTTTTGATGCTTCACATTCCTTATGG
+
;@@DDDDBHF?HAHCAFEEFF<<9CDDGEGHCFGF
@DBRHHJN1:175:C011MACXX:3:1101:1087:1093 1:N:0:ATCACG
TCACGAGTCAAGCTAACATAGCTTGTGAAAAGCCT
+
@@@FFDDD>DFHFFEEEGHIIEHHIIH@GGGGGEH

Thanks!

"

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by tiago2112871.1k

Thanks, I did see that post but it is not helpful because it discusses GAPfiller really. The error can't be with bwa because I have used bwa to align the reads in that file to lots of different template sequences. the problem must have something to do perhaps with the rest of the library file line for SSPACE.

 

Susanne

ADD REPLYlink written 4.2 years ago by susannehoward90

I tried to run the example as given in the SSPACE tutorial and get the same error:

Legacy library getopts.pl will be removed from the Perl core distribution in the next major release. Please install the separate libperl4-corelibs-perl package. It is being used at SSPACE_Standard_v3.0.pl, line 124.
ERROR: Invalid file in library lib1: SRR001665_1.fastq -- fatal

Susanne

ADD REPLYlink written 4.2 years ago by susannehoward90

I'm getting the same error, did you have any luck in solving this?

ADD REPLYlink written 4.0 years ago by Daniel3.7k

You can try to change the aligner in the library file, for example, bowtie or bwasw. I remember sometimes SSPACE will have some troblue with one of the aligners. Or you can use older version of SSPACE.

ADD REPLYlink written 2.8 years ago by caizexi12360
0
gravatar for psthomas
2.8 years ago by
psthomas0
psthomas0 wrote:

The solution looks like it will be a small change to the code that AssemblyImprover uses to generate the SSPACE config file.

See for discussion and best approach for a fix: https://github.com/sanger-pathogens/assembly_improvement/issues/67

ADD COMMENTlink written 2.8 years ago by psthomas0
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