Open dcopetti opened 5 years ago
Update: I am able to run it with the (link to the) fastq in the same folder:
/data/dario/bin/Scaff10X/src/scaff10x -nodes 15 -longread 0 -gap 100 -matrix 2000 -reads 10 -score 30 -edge 10000 -link 10 -block 50000 -plot barcode_lengtg.png Rabiosa_genome_v2.2.fa L6_R1.fq.gz L6_R2.fq.gz L7_R1.fq.gz L7_R2.fq.gz Rabv2_Scaff10x_test
Input target assembly file2: /data/dario/scaffolding_Rabv2/Rabiosa_genome_v2.2.fa
Input read1 file: /data/dario/scaffolding_Rabv2/L6_R1.fq.gz
Input read2 file: /data/dario/scaffolding_Rabv2/L6_R2.fq.gz
[bwa_index] Pack FASTA... ^CError running command: /data/dario/bin/Scaff10X/src/scaff-bin/bwa index tarseq.fastq > try.out
but if I put the symlinks (with the absolute path) on the input.dat file, I get the same error.
I have two pairs of input fastq files, and as you see above here, just the first pair is considered. How do I set up the .dat file correctly? Thanks!
Sorry about this problem and hopefully the issue has been sorted out. The reason was that I copy an aligned file to test the code, but wanted to avoid alignment. After that I forgot to change back. Now the issue is gone. Just re-install the code and try it again:
git clone https://github.com/wtsi-hpag/Scaff10X.git cd Scaff10X ./install.sh
Let me know if you have any problems.
Kind regards,
Zemin
Hello,
I would like to run Scaff10x, but after a minute or so that is running, I get this error:
though the file is there and I can run stat on it:
can you help me figure out the issue? Thanks,
Dario