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wtsi-hpag / Scaff10X

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
MIT License
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scaff_screeN not found #20

Open hyperoplus opened 3 years ago

hyperoplus commented 3 years ago

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?

andreaswallberg commented 3 years ago

I have the same issue. @hyperoplus did you solve it?

andreaswallberg commented 3 years ago

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 :-)

hyperoplus commented 3 years ago

Hi Andreas, many thanks for pointing this out, didn't notice this in the documentation.

It seems to be running ok now!

andreaswallberg commented 3 years ago

@hyperoplus

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!