biochristmas

Thank you for your reply. I also tried the '--fl_data' parameter today, and the number of transcripts in the GTF file is the same as when not using '--fl_data'. There...

@YaoYinYing Hi, I installed Umol based on the folk you provided, but encountered the error shown in the screenshot during the test run. Could you please provide some suggestions for...

@YaoYinYing Thank you very much for your advice. I will try to contact the administrator and address the issue.

@andrewprzh , I am using version 3.4.1 of IsoQuant。I have a new question: I noticed that when I run this command to expand transcript annotations on the reference genome: isoquant.py...

Hi, thank you for your reply. Here is my operating system and environment information, which I hope will help with resolving the issue. $ uname -a Linux mgt19 3.10.0-1160.el7.x86_64 #1...

Sure, the output of ls ./colabfold_db/ is ”COLABDB_READY colabfold_envdb_202108_aln.tsv colabfold_envdb_202108_db colabfold_envdb_202108_db_aln colabfold_envdb_202108_db_aln.dbtype colabfold_envdb_202108_db_aln.index colabfold_envdb_202108_db.dbtype colabfold_envdb_202108_db.GPU_READY colabfold_envdb_202108_db_h colabfold_envdb_202108_db_h.dbtype colabfold_envdb_202108_db_h.index colabfold_envdb_202108_db.idx colabfold_envdb_202108_db.idx.dbtype colabfold_envdb_202108_db.idx.index colabfold_envdb_202108_db.index colabfold_envdb_202108_db.lookup colabfold_envdb_202108_db_seq colabfold_envdb_202108_db_seq.dbtype colabfold_envdb_202108_db_seq_h colabfold_envdb_202108_db_seq_h.dbtype colabfold_envdb_202108_db_seq_h.index colabfold_envdb_202108_db_seq.index colabfold_envdb_202108_h.tsv...

"prefilter mark_test/test/prof_res colabfold_db_GPU/pdb100_230517.idx mark_test/test/tmp2/2421078915233214753/pref_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -k 0 --target-search-mode 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 300 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --cov-mode 0...

Hi, thank you for your response. I followed your suggestions and adjusted the parameters, but I'm still encountering errors. However, the error message seems to have changed. I used the...

Thank you very much for your response. The issue has been resolved after updating ColabFold. However, I noticed that when using the --use-templates and --af3-json parameters, the generated JSON file...