Closed aprezvykh closed 5 years ago
Hi,
Seems that "dwil" genome you specified in the recipe was not found in HAL. Could be for two reasons: (i) its name in HAL is different or (ii) it wasn't aligned at all / alignment is very fragmented. You can check the genome names in HAL with halStats
utility from HAL tools.
If the name is correct, then the genome is likely too fragmented / distant to produce meaningful alignment. In this case, just remove it from the comparison (just from the recipe, no need to recompute the alignment). In general, I recommend to use 3-4 closest references at once (12 is likely too many).
Thanks, i will try! P.S. Приятно увидеть отечественный софт, при этом еще софт, который реально искал.
Good morning.
I've tried to run Ragout with your fixes. I reduced number of ref.genomes to three. But i've got the same error as previous: ERROR: No sequences read for genome dwil
halStats output:
Anc0, 4, 12602538, 5956, 0, 510556
dvir_9, 0, 178684636, 762, 2304654, 0
dmoj, 0, 193826310, 6841, 6841, 0
dvir, 0, 206026697, 13530, 13530, 0
dgri, 0, 200467819, 17440, 17440, 0
All seems to be fine...Theese genomes are not far from each other, alignment should not be fragmented.
Thank you!
Hi,
Looks like the dwill
genome is not in the HAL alignment -- it should contain all genomes (references and target) that you specified in the recipe file.
Best, Mikhail
Closing due to inactivity, feel free to reopen if you have more questions.
Hello! I am trying to run ragout with large genome of Drosophila Virilis (~160 Gb), so i use HAL file, produced with ProgressiveCactus software
ProgressiveCactus run command:
~/sofware/progressiveCactus/bin/./runProgressiveCactus.sh hal.cfg hal/ alignment.hal --maxCpus=64 --maxThreads=64
ProgressiveCactus config file:
dana /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dana-all-chromosome-r1.05.fasta dere /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dere-all-chromosome-r1.05.fasta dgri /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dgri-all-chromosome-r1.05.fasta dmel /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dmel-all-chromosome-r6.19.fasta dmoj /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dmoj-all-chromosome-r1.04.fasta dper /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dper-all-chromosome-r1.3.fasta dpse /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dpse-all-chromosome-r3.04.fasta dsec /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dsec-all-chromosome-r1.3.fasta dsim /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dsim-all-chromosome-r2.02.fasta dvir /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dvir-all-chromosome-r1.06.fasta dwil /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dwil-all-chromosome-r1.05.fasta dyak /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/dyak-all-chromosome-r1.05.fasta dvir_9 /mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/masurca.allreads.fasta
HAL file was produced with no errors, so i run Ragout:
~/sofware/Ragout/ragout.py -t 64 -s hal ass.rcp
Ragout recipe file:
.references=dana,dere,dgri,dmel,dmoj,dper,dpse,dsec,dsim,dvir,dyak,dwil .target=dvir_9 .blocks=small .hal=/mnt/raid/illumina/AlexR/genomes/assemblies.nov.2018/9/report/ragout/alignment.hal
So i got the following log:
[15:37:03] INFO: Starting Ragout v2.0 [15:37:03] INFO: Synteny block scale set to 'small' [15:37:03] INFO: Extracting FASTA from HAL [15:37:06] INFO: Converting HAL to MAF [15:37:57] INFO: Extracting synteny blocks from MAF [15:37:57] INFO: Running maf2synteny module [15:38:05] INFO: Inferring phylogeny from synteny blocks data [15:38:05] ERROR: An error occured while running Ragout: [15:38:05] ERROR: No sequences read for genome dwil. Check recipe for correctness.
What can produce this error, and how can i solve it?