vinita Lamba

Hi @CJ-Chen I `git clone` your repo on my linux mechine. When I tried to run `./Linux.sh` or `java -Xmx2G -jar TBtools_JRE1.6.jar` it is giving error regarding update. I tried...

Hi I am using repeatMasker to mask my de novo genome, and assembly is at scaffold level. When I ran the repeatmasker with following command : `RepeatMasker -xsmall /path/genome.fa `...

No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment

2

Dear Authors, Thanks for the great tool. I am using this tool to assemble de novo vertebrate genome. I got the following file after running ` juicer pre -a -o...

HAL alignments and chaining: post processing TOGA outputs

10

Hi Dr. @MichaelHiller I have couple of queries regarding my TOGA outputs. I am working with vertebrates genomes (size ranging from 550Mb to 1Gb, all genomes that I considered are...

Cache entry deserialization failed, entry ignored

7

Hi Authors, I was able to run TOGA on my couple of species, but somehow, after running for 11 hours, I got this error for one of my species in...

V2 pipeline errors (cat_step; with my data NOT with test_data); V1 pipeline error:pipeline crashed

5

Hi @kirilenkobm @MichaelHiller, I `wget` [https://github.com/hillerlab/make_lastz_chains/archive/refs/heads/main.zip](https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fhillerlab%2Fmake_lastz_chains%2Farchive%2Frefs%2Fheads%2Fmain.zip&data=05%7C02%7Cvlamba%40uark.edu%7C9309e58fafc84524105308dc2c41650d%7C79c742c4e61c4fa5be89a3cb566a80d1%7C0%7C0%7C638433906582093870%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Q7w%2Bl30SYZ3Jm4jBmXxuIIMAUNFyoRIRBbe1IazzbD0%3D&reserved=0) installed all dependencies 1. Able to run make_chains.py successfully on test_data and got chained alignment BUT when I tried with my own data 2....

Hi Authors I tried the V1 of this pipeline but got the following error. [d1/4aa5ff] NOTE: Process `execute_jobs (334)` terminated with an error exit status (127) -- Execution is retried...

Hi authors, I ran the `./make_chains.py Cot Dis /home/vlamba/target.fa /storage/vlamba/data/Genomes-noto/NOTO-genome/query.fa --project_dir /home/vlamba/CotDis_chaining -f --chaining_memory 30` and got the following error: `### Nextflow process lastz finished successfully Found 8 output files...

Post-TOGA queries related to UL (Uncertain loss) and L (loss) status

2

Hello Dr. @MichaelHiller Greetings, I have some post toga queries: I am struggling with "L" and "UL" dataset. Please consider the following tree, where my research interest in not a...