ogrecio
commented
5 years ago I tried with different option parameters, assigning less memory (although thats shouldn't be a problem because I can allocate up to 120Gb per job). It stopped at the same point. Then I tried to restart it and got this error message:
canu -p ONTassembly -d $WDR -fast -minReadLength=1500 -stopOnLowCoverage=0.010 -redMemory=64 -oeaMemory=64 -batMemory=64 -merylMemory=64 -mhapMemory=64 -maxMemory=64 -mhapThreads=20 -maxThreads=20 -genomeSize=100m -gridEngineArrayMaxJobs=20 gridOptions="--time=8:00:00 --partition=shared --qos=shared --mem=80GB" -nanopore-raw METALGEN_cleaned_withshorter.fastq
-- Canu 1.8
--
-- CITATIONS
--
-- 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
--
-- Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM.
-- De novo assembly of haplotype-resolved genomes with trio binning.
-- Nat Biotechnol. 2018
-- https//doi.org/10.1038/nbt.4277
--
-- Read and contig alignments during correction, consensus and GFA building 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
--
-- 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 '1.8.0_181' (from '/opt/cesga/easybuild-cesga/software/Core/jdk/8u181/bin/java') with -d64 support.
--
-- WARNING:
-- WARNING: Failed to run gnuplot using command 'gnuplot'.
-- WARNING: Plots will be disabled.
-- WARNING:
--
-- Detected 24 CPUs and 126 gigabytes of memory.
-- Limited to 64 gigabytes from maxMemory option.
-- Limited to 20 CPUs from maxThreads option.
-- Detected Slurm with 'sinfo' binary in /bin/sinfo.
-- Detected Slurm with 'MaxArraySize' limited to 10000 jobs.
--
-- Found 322 hosts with 24 cores and 120 GB memory under Slurm control.
-- Found 7 hosts with 24 cores and 60 GB memory under Slurm control.
-- Found 10 hosts with 4 cores and 30 GB memory under Slurm control.
-- Found 52 hosts with 20 cores and 60 GB memory under Slurm control.
-- Found 8 hosts with 20 cores and 120 GB memory under Slurm control.
-- Found 1 host with 128 cores and 3906 GB memory under Slurm control.
--
-- (tag)Threads
-- (tag)Memory |
-- (tag) | | algorithm
-- ------- ------ -------- -----------------------------
-- Grid: meryl 64 GB 8 CPUs (k-mer counting)
-- Grid: hap 12 GB 8 CPUs (read-to-haplotype assignment)
-- Grid: cormhap 64 GB 20 CPUs (overlap detection with mhap)
-- Grid: obtmhap 64 GB 20 CPUs (overlap detection with mhap)
-- Grid: utgmhap 64 GB 20 CPUs (overlap detection with mhap)
-- Grid: ovb 4 GB 1 CPU (overlap store bucketizer)
-- Grid: ovs 8 GB 1 CPU (overlap store sorting)
-- Grid: red 64 GB 6 CPUs (read error detection)
-- Grid: oea 64 GB 1 CPU (overlap error adjustment)
-- Grid: bat 64 GB 8 CPUs (contig construction with bogart)
-- Grid: gfa 8 GB 8 CPUs (GFA alignment and processing)
--
-- In 'ONTassembly.seqStore', found Nanopore reads:
-- Raw: 8172601
-- Corrected: 0
-- Trimmed: 0
--
-- Generating assembly 'ONTassembly' in '/mnt/lustre/scratch/home/otras/ini/ogr/Metagenomics/HybridAssembly'
--
-- Parameters:
--
-- genomeSize 100000000
--
-- Overlap Generation Limits:
-- corOvlErrorRate 0.3200 ( 32.00%)
-- obtOvlErrorRate 0.1200 ( 12.00%)
-- utgOvlErrorRate 0.1200 ( 12.00%)
--
-- Overlap Processing Limits:
-- corErrorRate 0.5000 ( 50.00%)
-- obtErrorRate 0.1200 ( 12.00%)
-- utgErrorRate 0.1200 ( 12.00%)
-- cnsErrorRate 0.2000 ( 20.00%)
----------------------------------------
-- Starting command on Tue Mar 5 14:14:41 2019 with 231123.73 GB free disk space
cd /mnt/lustre/scratch/home/otras/ini/ogr/Metagenomics/HybridAssembly
sbatch \
--mem-per-cpu=4g \
--cpus-per-task=1 \
--time=8:00:00 \
--partition=shared \
--qos=shared \
--mem=80GB \
-D `pwd` \
-J 'canu_ONTassembly' \
-o canu-scripts/canu.07.out canu-scripts/canu.07.sh
sbatch: error: Batch script is empty!
-- Finished on Tue Mar 5 14:14:41 2019 (furiously fast) with 231123.73 GB free disk space
----------------------------------------
ERROR:
ERROR: Failed with exit code 1. (rc=256)
ERROR:
CRASH:
CRASH: Canu 1.8
CRASH: Please panic, this is abnormal.
ABORT:
CRASH: Failed to submit script.
CRASH:
CRASH: Failed at /mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Compiler/gcc/6.4.0/canu/1.8/bin/../lib/site_perl/canu/Execution.pm line 780.
CRASH: canu::Execution::submitScript("ONTassembly", undef) called at /opt/cesga/easybuild-cesga/software/Compiler/gcc/6.4.0/canu/1.8/bin/canu line 771
CRASH:
CRASH: No log file supplied.
CRASH:
skoren
brianwalenz
Hi there, my canu process is stopping after cormhap. I restart the job, but the same error appeared.
Can't figure out what the problem is. Any help, please?
canu -p ONTassembly -d $WDR -fast -minReadLength=1500 -stopOnLowCoverage=0.010 -redMemory=100 -oeaMemory=100 -batMemory=100 -merylMemory=100 -mhapMemory=100 -ovbMemory=100 -ovsMemory=100 -maxMemory=100 -mhapThreads=10 -maxThreads=20 -genomeSize=100m -gridEngineArrayMaxJobs=20 gridOptions="--time=8:00:00 --partition=shared --qos=shared --mem=100GB" -nanopore-raw METALGEN_cleaned_withshorter.fastq
This is the canu.out file: