SSPACE file error

Question

[susannehoward]

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?

[tiago211287]

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 formation of the header may be the origin of the error, maybe something that bwa ignores.

Doesn't help 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!

[susannehoward]

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

[susannehoward]

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

[Daniel]

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

[caizexi123]

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.

Answer 1

[psthomas]

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