Error during execution of redundans about redundans

[lpryszcz]

Can you send me the command line you used and list the output directory ls -lah redundans_out?

[evolgenomology]

Here you go:
run1-j3-i3.2log.txt

~/src/redundans/redundans.py -v -i ~/src/redundans/redundans.py -v -i /GenomeData_telfordNAS/Ananus/Ananus-Philipp/trimmed_reads/*2kbp*_paired.fq.gz -f /GenomeData_telfordNAS/Ananus/Ananus-Philipp/lane_300bp_600bp_N300_N600_corrected.dipSPAdes/spades/lane_300bp_600bp_N300_N600_corrected.scaffolds.fasta -o /work/Ananus/redundans/run1-j3-i3 -j 3 --iters 3 2>>redundans/run1-j3-i3.2log

total 3.4G


drwxrwxr-x 3 philipp philipp 4.0K Oct  9 19:35 .
drwxrwxr-x 9 philipp philipp 4.0K Oct 26 10:15 ..
drwxrwxr-x 6 philipp philipp 4.0K Oct  9 19:27 _sspace.1.1
lrwxrwxrwx 1 philipp philipp  151 Oct  9 16:52 contigs.fa -> /GenomeData_telfordNAS/Ananus/Ananus-Philipp/lane_300bp_600bp_N300_N600_corrected.dipSPAdes/spades/lane_300bp_600bp_N300_N600_corrected.scaffolds.fasta
-rw-rw-r-- 1 philipp philipp  20K Oct  9 16:56 contigs.fa.amb
-rw-rw-r-- 1 philipp philipp 5.1M Oct  9 16:56 contigs.fa.ann
-rw-rw-r-- 1 philipp philipp 184M Oct  9 17:01 contigs.fa.bck
-rw-rw-r-- 1 philipp philipp 268M Oct  9 16:56 contigs.fa.bwt
-rw-rw-r-- 1 philipp philipp 2.9M Oct  9 16:58 contigs.fa.des
-rw-rw-r-- 1 philipp philipp 6.4M Oct  9 16:53 contigs.fa.fai
-rw-rw-r-- 1 philipp philipp  67M Oct  9 16:56 contigs.fa.pac
-rw-rw-r-- 1 philipp philipp  461 Oct  9 17:01 contigs.fa.prj
-rw-rw-r-- 1 philipp philipp 134M Oct  9 16:57 contigs.fa.sa
-rw-rw-r-- 1 philipp philipp 346K Oct  9 16:58 contigs.fa.sds
-rw-rw-r-- 1 philipp philipp 346K Oct  9 16:58 contigs.fa.ssp
-rw-rw-r-- 1 philipp philipp 1.1G Oct  9 17:01 contigs.fa.suf
-rw-rw-r-- 1 philipp philipp 268M Oct  9 16:58 contigs.fa.tis
-rw-rw-r-- 1 philipp philipp 259M Oct  9 17:48 contigs.reduced.fa
-rw-rw-r-- 1 philipp philipp  20K Oct  9 17:51 contigs.reduced.fa.amb
-rw-rw-r-- 1 philipp philipp 4.2M Oct  9 17:51 contigs.reduced.fa.ann
-rw-rw-r-- 1 philipp philipp 257M Oct  9 17:51 contigs.reduced.fa.bwt
-rw-rw-r-- 1 philipp philipp 5.3M Oct  9 17:48 contigs.reduced.fa.fai
-rw-rw-r-- 1 philipp philipp  65M Oct  9 17:51 contigs.reduced.fa.pac
-rw-rw-r-- 1 philipp philipp 129M Oct  9 17:52 contigs.reduced.fa.sa
-rw-rw-r-- 1 philipp philipp    0 Oct  9 19:31 _reads.lane_5_2kbp_forward_paired.fq
-rw-rw-r-- 1 philipp philipp    0 Oct  9 19:31 _reads.lane_5_2kbp_reverse_paired.fq
-rw-rw-r-- 1 philipp philipp    0 Oct  9 19:33 _reads.lane_6_2kbp_forward_paired.fq
-rw-rw-r-- 1 philipp philipp    0 Oct  9 19:33 _reads.lane_6_2kbp_reverse_paired.fq
lrwxrwxrwx 1 philipp philipp   45 Oct  9 19:30 _sspace.1.1.fa -> _sspace.1.1/_sspace.1.1.final.scaffolds.fasta
-rw-rw-r-- 1 philipp philipp 1.4M Oct  9 19:31 _sspace.1.1.fa.fai
-rw-rw-r-- 1 philipp philipp    0 Oct  9 19:35 _sspace.1.1._gapcloser.1.1.fa
-rw-rw-r-- 1 philipp philipp    0 Oct  9 19:35 _sspace.1.1._gapcloser.1.1.fa.fai
-rw-rw-r-- 1 philipp philipp 1.1K Oct  9 19:35 _sspace.1.1._gapcloser.1.1.fa.log
-rw-rw-r-- 1 philipp philipp  474 Oct  9 19:35 _sspace.1.1._gapcloser.1.conf
-rw-rw-r-- 1 philipp philipp 374M Oct  9 18:35 _sspace.1.1.lib1.tab
-rw-rw-r-- 1 philipp philipp  95K Oct  9 18:35 _sspace.1.1.lib1.tab.log
-rw-rw-r-- 1 philipp philipp 388M Oct  9 19:22 _sspace.1.1.lib2.tab
-rw-rw-r-- 1 philipp philipp  98K Oct  9 19:22 _sspace.1.1.lib2.tab.log
-rw-rw-r-- 1 philipp philipp  106 Oct  9 19:22 _sspace.1.1.libs.txt
-rw-rw-r-- 1 philipp philipp 282K Oct  9 19:30 _sspace.1.1.sspace.log

[lpryszcz]

_sspace.1.1._gapcloser.1.1.fa is empty, most likely GapCloser failed. This is most due to empty .fq files as all your reads were removed due to quality filtering. This is properly handled in newer version I'm preparing. In meantime you can run redundans with --nogapclosing flag.

Or you can try newer version, but it's still experimental.

git clone -b make --recursive https://github.com/lpryszcz/redundans.git
cd redundans
(cd bin/bwa && make clean && make)
(cd bin/last && make clean && make)

[evolgenomology]

Thanks. I'll actually got a new scaffolding by excluding the buggy mate pair reads (only 75% were flagged as correct, so 25% paired end contamination). So I'll try the new version and compare to my current scaffolding.