adonis316
commented
7 months ago Can you check whether the files XXX.ont.fasta, XXX.ont.0.0.fasta are empty or not? If XXX.ont.fasta is empty, then racon will not run since there are no long reads waiting to be corrected.
Thanks, Mengyang
Dear Developer: I encountered a problem that the pipeline always stop in the racon correction step. It exits without any suggestions. Below are my codes: tgsgapcloser --scaff "/home/scaffolds.fa" --reads ../../1_cleandata/hifi.fasta --output hap2 --minmap_arg '-x asm20' --tgstype pb --racon "/home/miniconda3/pkgs/racon-1.5.0-h21ec9f0_2/bin/racon" --r_round 3 --thread 32 > pipe.log 2> pipe.err Here are the pipe.log : INFO : Run tgsgapcloser. from /home/miniconda3/bin ; Version : 1.2.1 ; Release time : 2022-12-30 . INFO : Parsing args starting ... --scaff /home/scaffolds.fa --reads ../../1_cleandata/hifi.fasta --output hap2 --minmap_arg -x asm20 --tgstype pb --racon /home/miniconda3/pkgs/racon-1.5.0-h21ec9f0_2/bin/racon --r_round 3 --thread 32
INFO : Parsing args end .
INFO : Checking basic args & env ...
INFO : Checking basic args & env end.
INFO : Step 1 , run TGSSeqSplit to split scaffolds into scaftigs(contigs). skip step1 since done_step1_tag exists
INFO : Step 1 , done .
INFO : Step 2 , run TGSCandidate ... skip step2.1 since done_step2.1_tag exists skip step2.2 since done_step2.2_tag exists skip step2.3 since done_step2.3_tag exists
INFO : Step 2 , done .
INFO : Step 3.A , error correction by racon ...
iteration 0 chunk 0 - racon ...
I wonder if you could help me with that.