Hi,
Thank you for the great tool. I want to use an ONT long-read to assemble the mtDNA of Spirodela polyrhiza. I have the following error. How can I change the option of PMAT to pass the error message.
Thank you,
SangChul
The error message is:
nextDenovo for correction and assembly end.
2024-10-02 14:26:56
Reads trim start ...
2024-10-02 14:26:59
-- canu 2.2
--
-- CITATIONS
--
-- For 'standard' assemblies of PacBio or Nanopore reads:
-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.
-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
-- Genome Res. 2017 May;27(5):722-736.
-- http://doi.org/10.1101/gr.215087.116
--
-- Read and contig alignments during correction and consensus use:
-- Šošic M, Šikic M.
-- Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.
-- Bioinformatics. 2017 May 1;33(9):1394-1395.
-- http://doi.org/10.1093/bioinformatics/btw753
--
-- Overlaps are generated using:
-- Berlin K, et al.
-- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
-- Nat Biotechnol. 2015 Jun;33(6):623-30.
-- http://doi.org/10.1038/nbt.3238
--
-- Myers EW, et al.
-- A Whole-Genome Assembly of Drosophila.
-- Science. 2000 Mar 24;287(5461):2196-204.
-- http://doi.org/10.1126/science.287.5461.2196
--
-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:
-- Chin CS, et al.
-- Phased diploid genome assembly with single-molecule real-time sequencing.
-- Nat Methods. 2016 Dec;13(12):1050-1054.
-- http://doi.org/10.1038/nmeth.4035
--
-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:
-- Chin CS, et al.
-- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
-- Nat Methods. 2013 Jun;10(6):563-9
-- http://doi.org/10.1038/nmeth.2474
--
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '11.0.1' (from '/home/user/miniconda3/envs/polap/bin/java') without -d64 support.
-- Detected gnuplot version '5.4 patchlevel 5 ' (from 'gnuplot') and image format 'png'.
--
-- Detected 56 CPUs and 252 gigabytes of memory on the local machine.
--
-- Local machine mode enabled; grid support not detected or not allowed.
--
-- (tag)Concurrency
-- (tag)Threads |
-- (tag)Memory | |
-- (tag) | | | total usage algorithm
-- ------- ---------- -------- -------- -------------------- -----------------------------
-- Local: meryl 24.000 GB 8 CPUs x 7 jobs 168.000 GB 56 CPUs (k-mer counting)
-- Local: hap 12.000 GB 14 CPUs x 4 jobs 48.000 GB 56 CPUs (read-to-haplotype assignment)
-- Local: cormhap 13.000 GB 14 CPUs x 4 jobs 52.000 GB 56 CPUs (overlap detection with mhap)
-- Local: obtovl 8.000 GB 8 CPUs x 7 jobs 56.000 GB 56 CPUs (overlap detection)
-- Local: utgovl 8.000 GB 8 CPUs x 7 jobs 56.000 GB 56 CPUs (overlap detection)
-- Local: cor -.--- GB 4 CPUs x - jobs -.--- GB - CPUs (read correction)
-- Local: ovb 4.000 GB 1 CPU x 56 jobs 224.000 GB 56 CPUs (overlap store bucketizer)
-- Local: ovs 8.000 GB 1 CPU x 31 jobs 248.000 GB 31 CPUs (overlap store sorting)
-- Local: red 16.000 GB 4 CPUs x 14 jobs 224.000 GB 56 CPUs (read error detection)
-- Local: oea 8.000 GB 1 CPU x 31 jobs 248.000 GB 31 CPUs (overlap error adjustment)
-- Local: bat 64.000 GB 8 CPUs x 1 job 64.000 GB 8 CPUs (contig construction with bogart)
-- Local: cns -.--- GB 8 CPUs x - jobs -.--- GB - CPUs (consensus)
--
-- Found untrimmed corrected Nanopore reads in the input files.
--
-- Generating assembly 'PMAT' in '/mnt/user/figshare/Spirodela_polyrhiza/pmat/trim_out':
-- genomeSize:
-- 108000000
--
-- Overlap Generation Limits:
-- corOvlErrorRate 0.3200 ( 32.00%)
-- obtOvlErrorRate 0.1200 ( 12.00%)
-- utgOvlErrorRate 0.1200 ( 12.00%)
--
-- Overlap Processing Limits:
-- corErrorRate 0.3000 ( 30.00%)
-- obtErrorRate 0.1200 ( 12.00%)
-- utgErrorRate 0.1200 ( 12.00%)
-- cnsErrorRate 0.2000 ( 20.00%)
--
-- Stages to run:
-- only trim corrected reads.
--
--
-- Correction skipped; not enabled.
--
-- BEGIN TRIMMING
----------------------------------------
-- Starting command on Wed Oct 2 14:26:59 2024 with 1149.632 GB free disk space
cd .
./PMAT.seqStore.sh \
> ./PMAT.seqStore.err 2>&1
-- Finished on Wed Oct 2 14:27:10 2024 (11 seconds) with 1149.385 GB free disk space
----------------------------------------
--
-- In sequence store './PMAT.seqStore':
-- Found 21627 reads.
-- Found 1041628981 bases (9.64 times coverage).
-- Histogram of corrected reads:
--
-- G=1041628981 sum of || length num
-- NG length index lengths || range seqs
-- ----- ------------ --------- ------------ || ------------------- -------
-- 00010 123334 723 104283600 || 5088-10312 1261|------------------------------
-- 00020 101284 1661 208333343 || 10313-15537 2653|---------------------------------------------------------------
-- 00030 88289 2764 312561303 || 15538-20762 1857|---------------------------------------------
-- 00040 77585 4023 416657398 || 20763-25987 1507|------------------------------------
-- 00050 67796 5460 520857488 || 25988-31212 1270|-------------------------------
-- 00060 58896 7106 625026660 || 31213-36437 1213|-----------------------------
-- 00070 49421 9030 729187468 || 36438-41662 1140|----------------------------
-- 00080 38581 11395 833322338 || 41663-46887 1111|---------------------------
-- 00090 24609 14717 937473047 || 46888-52112 1132|---------------------------
-- 00100 5088 21626 1041628981 || 52113-57337 1079|--------------------------
-- 001.000x 21627 1041628981 || 57338-62562 990|------------------------
-- || 62563-67787 951|-----------------------
-- || 67788-73012 816|--------------------
-- || 73013-78237 706|-----------------
-- || 78238-83462 649|----------------
-- || 83463-88687 568|--------------
-- || 88688-93912 483|------------
-- || 93913-99137 419|----------
-- || 99138-104362 334|--------
-- || 104363-109587 254|-------
-- || 109588-114812 231|------
-- || 114813-120037 183|-----
-- || 120038-125262 138|----
-- || 125263-130487 152|----
-- || 130488-135712 124|---
-- || 135713-140937 81|--
-- || 140938-146162 86|---
-- || 146163-151387 53|--
-- || 151388-156612 36|-
-- || 156613-161837 38|-
-- || 161838-167062 27|-
-- || 167063-172287 19|-
-- || 172288-177512 20|-
-- || 177513-182737 12|-
-- || 182738-187962 7|-
-- || 187963-193187 10|-
-- || 193188-198412 5|-
-- || 198413-203637 3|-
-- || 203638-208862 2|-
-- || 208863-214087 2|-
-- || 214088-219312 0|
-- || 219313-224537 1|-
-- || 224538-229762 1|-
-- || 229763-234987 1|-
-- || 234988-240212 1|-
-- || 240213-245437 0|
-- || 245438-250662 0|
-- || 250663-255887 0|
-- || 255888-261112 0|
-- || 261113-266337 1|-
--
--
-- ERROR: Read coverage (9.64) lower than allowed.
-- ERROR: minInputCoverage = 10
-- ERROR:
-- ERROR: This could be caused by an incorrect genomeSize.
-- ERROR:
-- ERROR: You can force Canu to continue by decreasing parameter
-- ERROR: minInputCoverage. Be warned that the quality of corrected
-- ERROR: reads and/or contiguity of contigs will be poor.
--
ABORT:
ABORT: canu 2.2
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting. If that doesn't work, ask for help.
ABORT:
[ WARNING 2024-10-02 14:27:11 ] An error occurred during the trim process?
The script is:
PMAT autoMito -i SRR11472010.fastq -o pmat -st ont -g 108m -cs nextDenovo \
-np /home/user/bin/nextDenovo \
-cp /home/user/bin/canu \
-cfg nextdenovo.cfg -m
nextdenovo.cfg is:
[General]
job_type = local # local, slurm, sge, pbs, lsf
job_prefix = nextDenovo
task = correct # all, correct, assemble
rewrite = yes # yes/no
deltmp = yes
parallel_jobs = 20 # number of tasks used to run in parallel
input_type = raw # raw, corrected
read_type = ont # clr, ont, hifi
input_fofn = input.fofn
workdir = pmat
[correct_option]
read_cutoff = 1k
genome_size = 108m
sort_options = -m 20g -t 15
minimap2_options_raw = -t 8
pa_correction = 3
correction_options = -p 15
[assemble_option]
minimap2_options_cns = -t 8
nextgraph_options = -a 1
Hi,
Thank you for the great tool. I want to use an ONT long-read to assemble the mtDNA of Spirodela polyrhiza. I have the following error. How can I change the option of PMAT to pass the error message.
Thank you,
SangChul
The error message is:
The script is:
nextdenovo.cfg is: