Tag Archives: SparseAssembler

Assembly & Stats – SparseAssembler (k95) on Geoduck Sequence Data > Quast for Stats

Had a successful assembly with SparseAssembler k101, but figured I’d just tweak the kmer setting and throw it in the queue and see how it compares; minimal effort/time needed.

Initiatied an assembly run using SparseAssembler on our Mox HPC node on all of our geoduck genomic sequencing data:

Kmer size set to 95.

Slurm script: 20180423_sparse_assembler_kmer95_geoduck_slurm.sh

After the run finished, I copied the files to our server (Owl) and then ran Quast on my computer to gather some assembly stats, using the following command:


/home/sam/software/quast-4.5/quast.py 
-t 24 
--labels 20180423_sparse_k95 
/mnt/owl/Athaliana/20180423_sparseassembler_kmer95_geoduck/Contigs.txt 

Results:

SparseAssembler output folder: 20180423_sparseassembler_kmer95_geoduck/

SparseAsembler assembley (FastA; 15GB): 20180423_sparseassembler_kmer95_geoduck/Contigs.txt

Quast output folder: quast_results/results_2018_05_10_15_04_07

Quast report (HTML): quast_results/results_2018_05_10_15_04_07/report.html

I’ve embedded the Quast HTML report below, but it may be easier to view by using the link above.

Well, it’s remarkable how different this is than the previous SparseAssembler with k101 setting!

This assembly doesn’t have a single contig >50,000bp, while the previous one has four contigs over that threshold!

Definitely shows what a large impact the kmer setting in assembly software can have on the final assembly!

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Assembly – SparseAssembler (k 111) on Geoduck Sequence Data

Continuing to try to find the best kmer setting to work with SparseAssemlber after the last attempt failed due to a kmer size that was too large (k 131; which happens to be outside the max kmer size [127] for SparseAssembler), I re-ran SparseAssembler with an arbitrarily selected kmer size < 131 (picked k 111).

The job was run on our Mox HPC node.

Results:

Output folder:

Slurm output file:

This failed with the following error message:

Error! K-mer size too large!

Well, this is disappointing. Not entirely sure why this is the case, as it’s below the max kmer setting for SparseAssembler. However, I’m not terribly surprised, as this happened previously (only using NovaSeq data) with a kmer setting of 117.

I’ve posted an issue on the kmergenie GitHub page; we’ll see what happens.

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Assembly – SparseAssembler (k 131) on Geoduck Sequence Data

After some runs with kmergenie, I’ve decided to try re-running SparseAssembler using a kmer setting of 131.

The job was run on our Mox HPC node.

Results:

Output folder:

Slurm output file:

This failed with the following error message:

Error! K-mer size too large!

Looking into this, it’s because the maximum kmer size for kmergenie is 127! Doh!

It’d be nice if the program looked at that setting first before processign all the data files…

A bit disappointing, but I’ll give this a go with a lower kmer setting and see how it goes.

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Genome Assembly – SparseAssembler Geoduck Genomic Data, kmer=101

UPDATE 20180413

Assembly complete. See end of post for data locations.


UPDATE 20180410

Received a status update email:

SLURM Job_id=156637 Name=20180405_sparse_assembler_kmer101_geo Ended, Run time 4-20:17:08, CANCELLED, ExitCode 0

After talking to Steven, it turns out Mox was taken offline for maintenance, which killed all jobs (and access). Ugh.

Will restart tonight once Mox is back online.


OK, here we go! Initiatied an assembly run using SparseAssembler on our Mox HPC node on all of our geoduck genomic sequencing data:

Kmer size set to 101.

This is 118 files of sequencing data!! Fingers crossed…

Slurm script: 20180405_sparse_assembler_kmer101_geoduck_slurm.sh


#!/bin/bash
## Job Name
#SBATCH --job-name=20180405_sparse_assembler_kmer101_geo
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes (We only get 1, so this is fixed)
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=30-00:00:00
## Memory per node
#SBATCH --mem=500G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/scrubbed/samwhite/20180405_sparseassembler_kmer101_geoduck

/gscratch/srlab/programs/SparseAssembler/SparseAssembler 
LD 0 
NodeCovTh 1 
EdgeCovTh 0 
k 101 
g 15 
PathCovTh 100 
GS 2200000000 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_1.fastq 
i2 /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_2.fastq 
i1 /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_1.fastq 
i2 /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_2.fastq 
i1 /gscratch/scrubbed/samwhite/bgi_geoduck/151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_1.fastq 
i2 /gscratch/scrubbed/samwhite/bgi_geoduck/151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_2.fastq 
i1 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_1.fastq 
i2 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_2.fastq 
i1 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_1.fastq 
i2 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_2.fastq 
i1 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_1.fastq 
i2 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_2.fastq 
i1 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_1.fastq 
i2 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_2.fastq 
i1 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_1.fastq 
i2 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_2.fastq 
i1 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_1.fastq 
i2 /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-1_S1_L001_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-1_S1_L001_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2_S5_L002_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2_S5_L002_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-3_S9_L003_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-3_S9_L003_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-4_S13_L004_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-4_S13_L004_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5_S17_L005_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5_S17_L005_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-6_S21_L006_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-6_S21_L006_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-7_S25_L007_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-7_S25_L007_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8_S29_L008_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8_S29_L008_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R2_001_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R1_001_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R2_001_val_2.fastq
Results:

Output folder: 20180405_sparseassembler_kmer101_geoduck/

Slurm output files:

SparseAssembler Assembly (FASTA): Contigs.txt

Added this to the GitHub wiki for our geoduck genome assemblies.

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Assembly – Geoduck NovaSeq using SparseAssembler kmer = 101

The prior run used a kmer size of 61, and the resulting assembly was rather poor (small N50).

For this run, I arbitrarily increased the kmer size to 101, in hopes that this will improve the assembly.

The job was run on our Mox node.

Here’s the batch script to initiate the job:

20180322_SparseAssembler_novaseq_geoduck_slurm.sh


#SBATCH --job-name=20180322_sparse_assembler_geo_novaseq
## Allocation Definition 
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes (We only get 1, so this is fixed)
#SBATCH --nodes=1   
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=30-00:00:00
## Memory per node
#SBATCH --mem=500G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/scrubbed/samwhite/20180322_SparseAssembler_novaseq_geoduck

/gscratch/srlab/programs/SparseAssembler/SparseAssembler 
LD 0 
NodeCovTh 1 
EdgeCovTh 0 
k 101 
g 15 
PathCovTh 100 
GS 2200000000 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fastq
Results

Output folder: 20180322_SparseAssembler_novaseq_geoduck/

This completed much more quickly than the previous run (kmer = 61). The previous assembly took ~10 days, while this assembly completed in ~4 days!

The primary output file of interest is this FASTA file:

In order to get a rough idea of how this assembly looks, I ran it through Quast Version: 4.5, 15ca3b9:

python software/quast-4.5/quast.py
-t 16
/mnt/owl/Athaliana/20180322_SparseAssembler_novaseq_geoduck/Contigs.txt

Quast output folder: results_2018_03_27_08_25_52/

Here’re the stats on the assembly:

Quast output (text): results_2018_03_27_08_25_52/report.txt

Quast output (HTML):results_2018_03_27_08_25_52/report.html

This is definitely a better assembly than the kmer = 61 assembly.

N50 = 1149

Also, there’s a single, large contig of 56,361bp, and 54 contigs > 25,000bp. This is good.

Admittedly, I’m a little surprised (and, disappointed) the N50 is as small as it is. However, we have a pretty decent assembly on our hands!

Since SparseAssembler seems to actually run (and, relatively quickly), I’m very tempted to just throw ALL of our geoduck data at it and see how it turns out…

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Assembly – Geoduck NovaSeq using SparseAssembler (TL;DR – it worked!)

The prior attempt using SparseAssembler failed due to a kmer size that was deemed too large.

For this run, I arbitrarily reduced the kmer size by ~half (k 61) in hopes that this will just get through an assembly. We can potentially explore the effects of kmer size on assemblies if/when this runs and depending no how the assembly looks.

The job was run on our Mox node.

Here’s the batch script to initiate the job:

#!/bin/bash
## Job Name
#SBATCH --job-name=20180313_sparse_assembler_geo_novaseq
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes (We only get 1, so this is fixed)
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=30-00:00:00
## Memory per node
#SBATCH --mem=500G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/scrubbed/samwhite/20180312_SparseAssembler_novaseq_geoduck

/gscratch/srlab/programs/SparseAssembler/SparseAssembler 
LD 0 
NodeCovTh 1 
EdgeCovTh 0 
k 61 
g 15 
PathCovTh 100 
GS 2200000000 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fastq
Results

Output folder: 20180312_SparseAssembler_novaseq_geoduck

IT WORKED!!! At last; we have an assembly of the geoduck NovaSeq data!! It took ~10days to complete.

The primary output file of interest is this FASTA file:

In order to get a rough idea of how this assembly looks, I ran it through Quast Version: 4.5, 15ca3b9:

python software/quast-4.5/quast.py
-t 16
/mnt/owl/Athaliana/20180312_SparseAssembler_novaseq_geoduck/Contigs.txt

Quast output folder: results_2018_03_22_08_12_12

Here’re the stats on the assembly:

Quast output (text): results_2018_03_22_08_12_12/report.txt

Quast output (HTML):results_2018_03_22_08_12_12/report.html

Overall, the assembly doesn’t look great. The N50 = 645 is really, really low. One would hope for a much large number for a quality assembly. As it stands, this assembly is comprised of many small contigs.

Looks like we’ll have to fiddle with the kmer size used for SparseAssembler and see if we can improve upon this.

Despite that, it’s an accomplishment to finally get any sort of assembler to run to completion for this data set!

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Assembly – Geoduck NovaSeq using SparseAssembler (failed)

Steven came across a 2012 paper in BMC Bioinformatics (“Exploiting sparseness in de novo genome assembly”) that utilized an assembly program we hadn’t previously encountered: SparseAssembler

This software is intended to greatly reduce the required amount of RAM necessary to process very large assembly data sets. As I previously learned, RAM is a limiting factor for assembly programs, and the install (if you can even call it that) was simply upacking a zip file (program installations on Mox are not trivialso this seems like it has promise!

The job was run on our Mox node.

Here’s the batch script to initiate the job:

20180308_soap_novaseq_geoduck_slurm.sh

#!/bin/bash
## Job Name
#SBATCH --job-name=20180308_sparse_assembler_geo_novaseq
## Allocation Definition 
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes (We only get 1, so this is fixed)
#SBATCH --nodes=1   
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=30-00:00:00
## Memory per node
#SBATCH --mem=500G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/scrubbed/samwhite/20180308_SparseAssembler_novaseq_geoduck

/gscratch/srlab/programs/SparseAssembler/SparseAssembler 
LD 0 
NodeCovTh 1 
EdgeCovTh 0 
k 117 
g 15 
PathCovTh 100 
GS 2200000000 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L002_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L001_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L001_R2_001_val_2_val_2.fastq 
i1 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L002_R1_001_val_1_val_1.fastq 
i2 /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fastq
Results

Output folder: 20180308_SparseAssembler_novaseq_geoduck/

Well, this failed, but not because of memory issues (which is a good start)!

Instead, it failed because the kmer size was too large??!!

See the slurm output log file:

Kmergenie had indicated a kmer size of 117bp.

Will reduce kmer size and try again. Fingers crossed…

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