lastal: can't interpret TAB

[apelin20]

Hello,

Ran into this error:

@BioPower3-IBM ~/programs/redundans $ ./redundans.py -v -i /shared/reads/Pseudoloma/GDR-24_R*_trim100.fastq -f ~/Pseudoloma/reads/mira_merged_sample50X_try1_out.unpadded_above500.fasta -o test/Pseudo_mira_100bp_Scaffold_try1 --sspacebin ~/programs/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl -t 8
Options: Namespace(fasta='/home/adrian/Pseudoloma/reads/mira_merged_sample50X_try1_out.unpadded_above500.fasta', fastq=['/shared/reads/Pseudoloma/GDR-24_R1_trim100.fastq', '/shared/reads/Pseudoloma/GDR-24_R2_trim100.fastq'], identity=0.51000000000000001, iters=2, joins=5, limit=0.20000000000000001, linkratio=0.69999999999999996, log=<open file '', mode 'w' at 0x7f84863ad1e0>, mapq=10, minLength=200, nocleaning=True, nogapclosing=True, noreduction=True, noscaffolding=True, outdir='test/Pseudo_mira_100bp_Scaffold_try1', overlap=0.66000000000000003, sspacebin='/home/adrian/programs/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl', threads=8, verbose=True)
Aligning 3594477 mates per library...
Insert size statistics Mates orientation stats
FastQ files median mean stdev FF FR RF RR
/shared/reads/Pseudoloma/GDR-24_R1_trim100.fastq /shared/reads/Pseudoloma/GDR-24_R2_trim100.fastq 264 265.46 14.71 1 9985 13 1

[Sat Mar 26 14:51:11 2016] Reduction...

file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]

lastal: can't interpret: TAB
test/Pseudo_mira_100bp_Scaffold_try1/contigs.fa 17972387 5935 0 0.00 0 0.00 0.000 0 17972387 100.00 5935 100.00
Aligning 3594477 mates per library...

[Sat Mar 26 14:51:40 2016] Scaffolding...
iteration 1.1 ...

It doesn't look like it removed redundancies. Any idea what is causing this?
Adrian

[lpryszcz]

which version of LAST are you using (lastal --version)?
I guess you need to update your LAST installation to version 700+.

[shyamrallapalli]

Yes it is an issue with LAST version,
in earlier version example 581-f uses different options
-f: output format: 0=tabular, 1=maf (1)
so lastal was not performed at all, it exits by printing
lastal: can't interpret: TAB

so i suggests couple of points
@lpryszcz could you please

1. indicate version of the softwares you recommend installing in README
2. implement some exception raising to alert such issues

[lpryszcz]

@shyamrallapalli I have included version in README. implementing exception raising will take a bit more time...

[shyamrallapalli]

nice 👍
and congratulations for the manuscript

[lpryszcz]

I have implemented LASTal version checking in the latest commit.