Comments (4)
I have the same issue. @hyperoplus did you solve it?
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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 :-)
from scaff10x.
Hi Andreas, many thanks for pointing this out, didn't notice this in the documentation.
It seems to be running ok now!
from scaff10x.
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!
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Related Issues (20)
- No scaffolding being done on the Scaff10xV4 HOT 4
- Segmentation fault HOT 24
- cannot find input.dat HOT 2
- can you update the docs to reflect the actual usage
- segfault HOT 10
- run fails at scaff_matrix HOT 8
- another seg fault issue HOT 6
- Floating point exception in break10x HOT 11
- segmentation fault HOT 8
- scaff_reads: Segmentation fault HOT 3
- scaff_bwa segmentation fault HOT 3
- pre n50 = scaff10x n50 HOT 1
- how does scaff_reads works
- "Numbers of contigs are difference," error in "scaff_bwa-barcode"
- add gnuplot and inkscape to install.sh
- segmentation fault scaff_bwa.c
- scaff10x still running after 22 days
- Pigz installation
- Scaffolding with parental reads
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