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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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i have installed syri using conda but after running iam getting error in reading sam file i have used minimap2 to convert fna file to sam file #207

Closed Hemaprasanth24 closed 10 months ago

Hemaprasanth24 commented 11 months ago

syri -c align.sam -r GCA_020546685.1_ASM2054668v1_genomic.fna -q GCA_002198095.1_ASM219809v1_genomic.fna -k -F S SAM reader - WARNING - NHMK01000003.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000021.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000015.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000029.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000016.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000012.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000009.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000023.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000018.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000006.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000004.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000034.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000001.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000040.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000039.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000019.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000020.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000027.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000002.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000007.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000013.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000008.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000035.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000031.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000011.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000036.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000033.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000005.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000037.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000038.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000024.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000010.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000017.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000026.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000014.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000028.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000025.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000030.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000022.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. SAM reader - WARNING - NHMK01000032.1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. Reading BAM/SAM file - ERROR - Unexpected error in opening BAM/SAM file. 6

mnshgl0110 commented 11 months ago

Syri works with chromosome-level assemblies. It seems that the query genome has scaffolds/contigs. Please read the documentation here: https://schneebergerlab.github.io/syri/

Hemaprasanth24 commented 11 months ago

In syri is it possible to apply more than one genome as query genome

On Tue, 8 Aug, 2023, 13:46 Manish Goel, @.***> wrote:

Syri works with chromosome-level assemblies. It seems that the query genome has scaffolds/contigs. Please read the documentation here: https://schneebergerlab.github.io/syri/

— Reply to this email directly, view it on GitHub https://github.com/schneebergerlab/syri/issues/207#issuecomment-1669135966, or unsubscribe https://github.com/notifications/unsubscribe-auth/A73BTRXLSZ5CTMMZDFF6B23XUHYWDANCNFSM6AAAAAA3HHCEFU . You are receiving this because you authored the thread.Message ID: @.***>

mnshgl0110 commented 10 months ago

Syri performs pairwise comparisons. So, one query vs one reference at a time. Of course, you can run syri multiple times with different query genomes. As the original problem is resolved, I am closing this issue. Please feel free to open new issues for other questions.

Hemaprasanth24 commented 10 months ago

Awesome, thanks for the update!

On Thu, Aug 10, 2023 at 2:47 PM Manish Goel @.***> wrote:

Closed #207 https://github.com/schneebergerlab/syri/issues/207 as completed.

— Reply to this email directly, view it on GitHub https://github.com/schneebergerlab/syri/issues/207#event-10056802156, or unsubscribe https://github.com/notifications/unsubscribe-auth/A73BTRW44DBEC6DRUVK4ZY3XUSRI5ANCNFSM6AAAAAA3HHCEFU . You are receiving this because you authored the thread.Message ID: @.***>