scaff_screeN not found
hyperoplus opened this issue · comments
Hi,
I'm trying to run Scaff10X (4.2) to assemble a set of contigs with 10X reads. However, right at the start I get the following problem:
Input:
./scaff10x -nodes 30 -longread 1 -gap 100 -matrix 2000 -reads 10 -score 20 -edge 50000 -link 8 -block 50000 -plot barcode_lengtg.png myassembly.fa R1.test.fq.gz R2.test.fq.gz output.test.fa
Output:
Input target assembly file2: /home/Scaff10X/src/myassembly.fa
Input read1 file: /home/Scaff10X/src/R1.test.fq.gz
Input read2 file: /home/Scaff10X/src/R2.test.fq.gz
sh: 1: ./scaff-bin/scaff_screeN: not found
Error running command: ./scaff-bin/scaff_screeN /home/Scaff10X/src/myassembly.fa cleaN.fasta > try.out
However, scaff_screeN is right where it should be, and even if I type ./scaff-bin/scaff_screeN
the prompt delivers a usage instruction, signalling the executable works: Usage: ./scaff-bin/scaff_screeN <input fast/aq file> <output fasta file>
I tried this in two separate Linux machines, both gave the same issue. Do you have any idea what could be happening?
I have the same issue. @hyperoplus did you solve it?
Dang! The solution is of course in the documentation:
The binary needs to be called using the full path:
/full/path/to/Scaff10X/src/scaff10X
Then it works for me :-)
Hi Andreas, many thanks for pointing this out, didn't notice this in the documentation.
It seems to be running ok now!
Glad I could help! Actually, can I ask for a favor as we both seem to be pushing our way through the tool chain for the first time?
I got stuck further into the process as I suspect that Scaff10x does not like the way my chromium barcodes are encoded in the BAM files (as "BX:Z:" tags) that I provide.
Can you please send a few lines of SAM read mappings that the program accepts (or generates itself if you give it fastq files) in your case, so that I can check what kind of reformatting I need to accomplish?
You can find my email under my profile. Cheers!