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Issues reading SAM file #20
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Hi. SyRI requires the CIGAR strings to have '=' for match and 'X' for mismatch. While running minimap2, please use |
Thanks! I clearly missed this when looking at the working example page in the documentation. I can now get syri to run (using the same command as above), but it's now apparently having issues with chromosome IDs (see error below). I'm also attaching the log file in case that is helpful.
Thanks! |
Can you please also share the corrected SAM file? Thanks |
MINF_9D_vs_MSB1_6J_minimap.sam.txt |
Hi Jane, thanks for sharing the file. There were some uncaught exceptions which were causing issues with your data ('genomes' without structural variations were not expected). I have modified the script and it should finish properly without complaining about it. Please download and re-install SyRI, and rerun the analysis. |
Thank you!
…On 21 Dec 2019, 12:03 AM +1100, Manish Goel ***@***.***>, wrote:
Hi Jane, thanks for sharing the file. There were some uncaught exceptions which were causing issues with your data ('genomes' without structural variations were not excepted). I have modified the script and it should finish properly without complaining about it. Please download and re-install SyRI, and rerun the analysis.
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Hi,
I'm currently attempting to test out syri but I'm having issues using a SAM file as input.
I've used minimap2 to align my two fasta files:
minimap2 -ax asm5 MINF_9D.fasta MSB1_6J.fasta > MINF_9D_vs_MSB1_6J_minimap.sam
I then pass this sam file to syri:
./syri/syri/bin/syri -c MINF_9D_vs_MSB1_6J_minimap.sam -r MINF_9D.fasta -q MSB1_6J.fasta -F S
However I get this error:
I can't see anything in the log file that might help me work out what's going on - I set the log level to debug, and this is what's inside the log file:
I'm attaching my sam file here, in case there's something in it that's preventing syri from reading it?
MINF_9D_vs_MSB1_6J_minimap.sam.txt
Any help you could give would be greatly appreciated!
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