no fake mate pairs created

[webbchen]

Dear Francesca

I've got a genome and a fastq file with Nanopore reads. It seems that the splitting into 2 fake mate pairs doesn't work, I'm getting 2 empty files with fakemates_1.fq and fakemates_2.fq, it then proceeds to index the genome alright with bwa index, makes a tiny bam file and then fails with:

./mysmissv.sh
./mysmissv.sh: line 94: 11340 Segmentation fault      $bindir/smis_shred -rlength $fakelen -step $step -minlen $minlen $fqfile fakemates_1.fastq fakemates_2.fastq >> $outp
./mysmissv.sh: line 143: 11429 Segmentation fault      $bindir/smis_sort bwa_sorted.bam &>> outp
wc: path/to/dir/tempWork/genome-matepair-*: No such file or directory
in files.txt: smalt (bwa) data line should be <filename> <insert size> <standard deviation> <weight> <read length> <orientation, must = "in" | "out">
mv: cannot stat ‘spinner-sp2b.fasta’: No such file or directory

 Scaffolds are in spinner_scaffolds.fasta
 Summary of parameters used are in  /path/to/dir/logs/launchedas_1529497860.txt
 Log is in  /path/to/dir/logs/output_1529497860.txt 

(path names anonymised)
The log output_1529497860.txt states:

################## Running Output ##################

Creating fake-mate pairs from long read fastq file

Preparing Reference Fasta file

Aligning Fake-Mate Pairs to References with BWA:

[bwa_index] Pack FASTA... 0.42 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=81105476, availableWord=17706840
[BWTIncConstructFromPacked] 10 iterations done. 29207572 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 53956932 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 75950212 characters processed.
[bwa_index] 23.12 seconds elapse.
[bwa_index] Update BWT... 0.25 sec
[bwa_index] Pack forward-only FASTA... 0.26 sec
[bwa_index] Construct SA from BWT and Occ... 14.46 sec
[bwt_gen] Finished constructing BWT in 33 iterations.
[main] Version: 0.7.12-r1039
[main] CMD: /scratch/software/bwa-0.7.12/bwa index genome.fasta
[main] Real time: 38.488 sec; CPU: 38.512 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[main] Version: 0.7.12-r1039
[main] CMD: /scratch/software/bwa-0.7.12/bwa mem -t 25 -T 50 -A 2 -O -1 -E -1 -B -1 genome.fasta fakemates_1.fastq fakemates_2.fastq
[main] Real time: 0.070 sec; CPU: 0.072 sec

  Sort Aligned Fake-Mate Pairs by their Position in Reference



Scaffolding Reference using Fake-Mate Pairs

################## Scaffolding ... ##################

.
The launchedas log launchedas_1529497860.txt states:

################# Settings Used for Running ##################
export MYSMISDIR=/scratch/software/smis

fasta file of assembly to scaffold

fafile=/some/file/path/to/fungus_draft_assembly.fasta

fastq file with long reads

fqfile=/some/file/path/to/fungus_trimmed.fastq

working directory

odir=/path/to/dir
##bin directory: where the executables are
bindir=$MYSMISDIR/smissv-bin

#which samtools
mysamtools=which samtools

running mode

debug=1

########### FAKE-MATES PARAMETERS: ###########

min length of long reads

minlen=3000

length of fake mates

fakelen=2000

distance between one fake mate pairs and the next

step=200

########### ALIGNMENT PARAMETERS: ###########

which aligner to use (bwa, smalt)

aligner=bwa

bwa

mybwa=which bwa

smalt

mysmalt=which smalt

max threads:

nodes=25

minimum smith-waterman alignment score to report a hit

mapscore=50

Alignment scores and penalties

match=2
subst=-1
gapopen=-1
gapext=-1

########### SCAFFOLDING PARAMETERS: ###########

minimum numbers of edges:

min_edge=5.0
num_sigma=awk "BEGIN {print ($min_edge)/2.5}"

(Paths to files and filenames anonymised.)
Are there any other logs I should have found?

The E.coli test completed fine.

Kind regards and many thanks,

Anne