No scaffolding being done on the Scaff10xV4 about scaff10x

[EdHarry]

I've just pushed an update with should have better error handling. Could you try the latest version out.

BTW, unless you want to keep the barcode processed reads, it will be more efficient to list your 10x fq files in an input.fofn text file and pass that in with -data input.fofn.

[harish0201]

Thank you for the update!

I did try having the list in the fofn and then pass it on. But I then broke down all the steps to see where the errors occurred!

I have manually generated the bwa indices and I'm currently doing the steps manually to further trouble shoot where the issues are.

I'll keep you updated.

[mwhj]

I have the same problem! I've been pulling my hair out thinking I've been doing something wrong. It would be really brilliant to get this fixed.

[harish0201]

Alright, I have finally a 10X dataset that I have to use to scaffold. These are the errors on the latest commit:

[main] CMD: /home/harish/Tools/Scaff10X/src/scaff-bin/bwa mem -t 30 tarseq.fastq /data/analysis/dr.n.v.singh/genome/10X/scaff/genome-BC2_1.fastq.gz /data/analysis/dr.n.v.singh/genome/10X/scaff/genome-BC2_2.fastq.gz [main] Real time: 43975.365 sec; CPU: 1319572.223 sec sh: -c: line 0: syntax error near unexpected token ('
sh: -c: line 0: mv genome.fasta /data/analysis/plant/genome/10X/scaff/(null)' Error running command: mv genome.fasta /data/analysis/plant/genome/10X/scaff/(null) Input target assembly file2: /data/analysis/plant/genome/10X/scaff/polished.fa Input read1 file: /data/analysis/plant/genome/10X/scaff/genome-BC2_1.fastq.gz Input read2 file: /data/analysis/plant/genome/10X/scaff/genome-BC2_2.fastq.gz /home/harish/Tools/Scaff10X/src/scaff-bin/bwa mem -t 30 tarseq.fastq /data/analysis/plant/genome/10X/scaff/genome-BC2_1.fastq.gz /data/analysis/plant/genome/10X/scaff/genome-BC2_2.fastq.gz | egrep tarseq_ | awk '($2<100)&&($5>=0){print $1,$2,$3,$4,$5}' | egrep -v '^@' > align.dat

It still generates a genome.fasta which seems to be after scaffolding, but there's very less reduction, which is kinda curious. I'll have to check with the older version.

Reg: Retaining the debar-coded reads, I plan to use them for polishing as well :) Thanks for the heads-up