gapless
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schmeing
Gapless provides combined scaffolding, gap-closing and assembly correction with long reads
Hi, I got an error in running gapless.sh (in the step of gapless.py extend); logs/gapless_extend.log describes the following error, "Traceback (most recent call last): File "/analysis/program/gapless.py", line 13362, in main(sys.argv[1:])...
Hello, I am using gapless with python version 3.9.6, and I get this error on the extend step: Traceback (most recent call last): File "/home/student.unimelb.edu.au/sbjornson/opt/gapless/gapless.py", line 13362, in main(sys.argv[1:]) File...
Hi! I'm having an issue running the script after installing with conda. This is the scaffold log file. 0:00:03.965568 Reading in original assembly 0:00:03.971603 Loading repeats Traceback (most recent call...
Hello, I had assembled my genome using Illumina and PacBio reads and then I wanted to gap fill using Oxford Nanopore. I was trying to run the following: gapless.sh -j...
gapless.py extend -p gapless gapless_extending_reads.paf 0:00:15.342579 Preparing data from files 0:13:51.708704 Searching for extensions Traceback (most recent call last): File "/home/zhuchenzhao/miniconda3/bin/gapless.py", line 13327, in main(sys.argv[1:]) File "/home/zhuchenzhao/miniconda3/bin/gapless.py", line 13193, in...
Dear Developer Excuse me, I already have a genome at the chromosome level, so I just want to try filling gap with GAPLESS. Do you think it's okay?
Hi, We've curated a region of about 2Mb of a mammalian genome but there is still a gap in it, of unknown length, which could be 200kb or longer. The...
I had an issue on the scaffolding step; probably allocating memory.... But I do not understand because the node I used is allocated 256Gb memory. Below is the error message...
Hi, Thank you for the great program. According to your manual, it says: gapless.sh -j 30 -i assembly.fa.gz -t pb_clr data_pacbio_clr.fq.gz gapless.sh -j 30 -i assembly.fa.gz -t pb_hifi data_pacbio_hifi.fq.gz gapless.sh...
Hi @schmeing I've tried troubleshooting with different conda installations and I can't get Gapless to run on my assembly. The command that fails and yields `pipeline crashed : scaffold` is...
