cannot find input.dat

[dcopetti]

Hello,

I would like to run Scaff10x, but after a minute or so that is running, I get this error:

[copettid@kp140-95 scaffolding_Rabv2]$ /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 -data input.dat Rabiosa_genome_v2.2.fa Rabv2_Scaff10x_test
Input target assembly file2: /data/dario/scaffolding_Rabv2/Rabiosa_genome_v2.2.fa
cp input.dat align.dat
cp: cannot stat 'input.dat': No such file or directory
Error running command: cp input.dat align.dat

though the file is there and I can run stat on it:

[copettid@kp140-95 scaffolding_Rabv2]$ ls -lrth
total 4.8G
-rwx------+ 1 copettid mpb 4.8G Jul 17 17:35 Rabiosa_genome_v2.2.fa
-rw-rw----+ 1 copettid mpb  324 Jul 17 17:38 input.dat 
[copettid@kp140-95 scaffolding_Rabv2]$ stat input.dat
  File: input.dat
  Size: 324             Blocks: 8          IO Block: 4096   regular file
Device: fd00h/64768d    Inode: 4299148105  Links: 1
Access: (0660/-rw-rw----)  Uid: (201168/copettid)   Gid: (217165/     mpb)
Access: 2019-07-17 17:38:42.055868594 +0200
Modify: 2019-07-17 17:38:42.055868594 +0200
Change: 2019-07-17 17:38:53.782943899 +0200
 Birth: -

can you help me figure out the issue?
Thanks,

Dario

[dcopetti]

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!

[zning-sanger]

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