error: overlap is not transmuted!
Closed this issue · 6 comments
Hello Racon,
I have recently run into this error while attempting to polish some contigs using primary reads filtered by the "tp:A:P" tag. Furthermore, this is using a minimap alignment with customized parameters. To give some background information these are the commands I ran:
Minimap2 alignment
time minimap2 -I 100G -c -t 96 -A 5 -B 1 -O 7,46 -E 28,13 -z 350,300 -s 220 ~/assembly/t2.dmo.lay.utg ~/raw_reads/ont/OS001288_PAG98861.pass.fastq.gz ~/raw_reads/ont/OS003D2E_PAH61301.pass.fastq.gz > pine_optimized_param_100G.base_level_alignment.paf
Racon polishing
time racon -t 96 ~/raw_data/merged_fastq/merged_fastq_test_set.fastq.gz ~/raw_data/pine_optimized_param_100G.base_level_alignment.prim_only.paf ~/raw_data/contigs/random_sample_100.fa > racon_w_paf.optimized_parameters_I_100G.base_level_alignment.prim_only.fasta
I am currently, using racon v1.4.20 on a conda installation in a SLURM environment. While using the default parameters for the minimap2 alignment I have had no issues. Additionally, running racon on the unfiltered file also causes no issues. However, when I used my custom parameters racon is unable to run polishing with the filtered file.
I have been referencing issue #77 in order to help solve the issue but, to no avail. I have attempted to reorganize the racon input files and I have validated that the reads and contigs exist in the alignment file. But, I am unable to find what's causing the error.
I was hoping to get your input on this? Thank you for your time!
Kind Regards,
Alex
Hi Alex,
your alignment/polishing commands have missmatching file names. Can you please paste the matching Racon command?
Best regards,
Robert
Hello Robert,
Thank you for pointing that out! To clarify, I ran the following command to filter for primary reads from the minimap2 alignment found above and used the resulting output file for the above racon step:
grep 'tp:A:P' ~/output/pine_optimized_param_100G.base_level_alignment.paf > ~/raw_data/pine_optimized_param_100G.base_level_alignment.prim_only.paf
Kind Regards,
Alex Lim
I suppose you combined OS001288_PAG98861.pass.fastq.gz and OS003D2E_PAH61301.pass.fastq.gz into merged_fastq_test_set.fastq.gz?
You are mapping the reads to t2.dmo.lay.utg but polishing random_sample_100.fa. What is their relation?
Hello Robert,
Yes sir, I combined them into a single file merged_fastq_test_set.fastq.gz. I actually wanted to ask you about this, will racon take a list of .fq.gz files or does it only take a single merged file?
As you mentioned I have t2.dmo.lay.utg and random_sample_100.fa. Random_sample_100.fa is a random subset of 100 contigs from t2.dmo.lay.utg. Just to clarify I am doing test runs before I apply the polishing to my entire dataset.
I hope this helps.
Kind Regards,
Alex
Due to argument order only one read file can be given to Racon. Can you please try the latest version by cloning the main repository https://github.com/lbcb-sci/racon?
Hello Robert,
I took your advice and tested the latest version of Racon, it seems the polishing has now gone through!
Kind Regards,
Alex