Comments (5)
Hi. It seems that there are two issues. First is that the program is crashing. And second is that too few SNPs were identified.
The first issue seems to be a bug. Can you please share the log file so that I could have more information about the run?
For the second issue, can you please check how many SNPs are identified when using the show-snps
utility from MUMmer? SyRI can only report SNPs which are identified by the MUMmer alignments. So, it would be worthwhile to first check whether are indeed SNPs present in the alignments or not. Additionally, please also upload the snps_GARB.txt file.
from syri.
show-snps produce 17107349。 The syri.log is blank.
from syri.
The snps_GARB.txt file. I sent to your email
from syri.
Hi. A blank log file is quite strange. That could mean that SyRI was not running properly at all. Could you please check the installation again, and also the command that you are using.
Also, I didn't receive any email. Could you please check that you used the right email address.
from syri.
There was a bug affecting SNP identification. It should be fixed now and you should be getting proper number of SNPs.
from syri.
Related Issues (20)
- Removes 'low-quality alignments' - what does this mean? HOT 1
- complicated region not detected correctly HOT 2
- About InvOut and Inv breakpoints HOT 3
- Huge chromosome problem HOT 6
- keyerror HOT 3
- Request for Guidance on Converting NOTALs to Presence in Syri Outputs HOT 3
- translocated to different chromosomes HOT 3
- Consult DUP/INVDP for details HOT 2
- microhomology at ends of insertions HOT 4
- INV vs INVDUP HOT 2
- ERROR syri:201 - Length of query sequence of Chr1 is less than the maximum coordinate of its aligned regions HOT 7
- Wrong CIGAR string HOT 1
- IndexError: list index out of range syri HOT 9
- SYRI:IndexError: list index out of range HOT 1
- how to merge SyRI vcfs HOT 2
- Questions about 'NOTAL' HOT 2
- Question about output
- Support for promer HOT 3
- CIGAR string starting with non-matching base HOT 1
- Overlapping INV and SYN HOT 3
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