Mox Fastqc And Minia
Playing around a bit with Mox (crippled by lack of disk space). Ran FastQC
#!/bin/bash
## Job Name
#SBATCH --job-name=fastqc-NS
## 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=24:00:00
## Memory per node
#SBATCH --mem=500G
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/0901
source /gscratch/srlab/programs/scripts/paths.sh
/gscratch/srlab/programs/FastQC/fastqc \
-t 28 \
/gscratch/scrubbed/sr320/AD002_S9_L001_R1_001.fastq.gz
and minia (note location)
#!/bin/bash
## Job Name
#SBATCH --job-name=minia
## 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=100:00:00
## Memory per node
#SBATCH --mem=500G
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/0901b
source /gscratch/srlab/programs/scripts/paths.sh
/gscratch/srlab/sr320/programs/minia-v2.0.7-bin-Linux/bin/minia \
-nb-cores 28 \
-max-memory 500000 \
-in /gscratch/scrubbed/sr320/AD002_S9_L001_R2_001.fastq.gz \
-out-dir /gscratch/scrubbed/sr320/
minia seems to create a lot of temporary files (probably could have wrote to scrubbed)
[sr320@mox1 0901b]$ ls
slurm-71843.out trashme_32333_dsk_partitions.parts.20 trashme_32333_dsk_partitions.parts.34 trashme_32333_dsk_partitions.parts.48
slurm-71844.out trashme_32333_dsk_partitions.parts.21 trashme_32333_dsk_partitions.parts.35 trashme_32333_dsk_partitions.parts.49
trashme_32333_dsk_partitions.parts.0 trashme_32333_dsk_partitions.parts.22 trashme_32333_dsk_partitions.parts.36 trashme_32333_dsk_partitions.parts.5
trashme_32333_dsk_partitions.parts.1 trashme_32333_dsk_partitions.parts.23 trashme_32333_dsk_partitions.parts.37 trashme_32333_dsk_partitions.parts.50
trashme_32333_dsk_partitions.parts.10 trashme_32333_dsk_partitions.parts.24 trashme_32333_dsk_partitions.parts.38 trashme_32333_dsk_partitions.parts.51
trashme_32333_dsk_partitions.parts.11 trashme_32333_dsk_partitions.parts.25 trashme_32333_dsk_partitions.parts.39 trashme_32333_dsk_partitions.parts.52
trashme_32333_dsk_partitions.parts.12 trashme_32333_dsk_partitions.parts.26 trashme_32333_dsk_partitions.parts.4 trashme_32333_dsk_partitions.parts.53
trashme_32333_dsk_partitions.parts.13 trashme_32333_dsk_partitions.parts.27 trashme_32333_dsk_partitions.parts.40 trashme_32333_dsk_partitions.parts.54
trashme_32333_dsk_partitions.parts.14 trashme_32333_dsk_partitions.parts.28 trashme_32333_dsk_partitions.parts.41 trashme_32333_dsk_partitions.parts.55
trashme_32333_dsk_partitions.parts.15 trashme_32333_dsk_partitions.parts.29 trashme_32333_dsk_partitions.parts.42 trashme_32333_dsk_partitions.parts.6
trashme_32333_dsk_partitions.parts.16 trashme_32333_dsk_partitions.parts.3 trashme_32333_dsk_partitions.parts.43 trashme_32333_dsk_partitions.parts.7
trashme_32333_dsk_partitions.parts.17 trashme_32333_dsk_partitions.parts.30 trashme_32333_dsk_partitions.parts.44 trashme_32333_dsk_partitions.parts.8
trashme_32333_dsk_partitions.parts.18 trashme_32333_dsk_partitions.parts.31 trashme_32333_dsk_partitions.parts.45 trashme_32333_dsk_partitions.parts.9
trashme_32333_dsk_partitions.parts.19 trashme_32333_dsk_partitions.parts.32 trashme_32333_dsk_partitions.parts.46
trashme_32333_dsk_partitions.parts.2 trashme_32333_dsk_partitions.parts.33 trashme_32333_dsk_partitions.parts.47
[sr320@mox1 0901b]$ tail slurm-71844.out
[DSK: Collecting stats on AD002_S9_L... ] 100 % elapsed: 0 min 47 sec estimated remaining: 0 min 0 sec cpu: 243.5 % mem: [ 73, 73, 73] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 82.8 % elapsed: 17 min 8 sec estimated remaining: 3 min 34 sec cpu: 368.9 % mem: [43863, 43863, 43865] MB
slurm tail
minia
-nb-cores : 28
-max-memory : 500000
-in : /gscratch/scrubbed/sr320/AD002_S9_L001_R2_001.fastq.gz
-out-dir : /gscratch/scrubbed/sr320/
-traversal : contig
-starter : best
-contig-max-len : 10000000
-bfs-max-depth : 500
-bfs-max-breadth : 20
-fasta-line : 0
-kmer-size : 31
-abundance-min : 3
-abundance-max : 4294967295
-histo-max : 10000
-solidity-kind : sum
-max-disk : 0
-minimizer-type : 0
-minimizer-size : 8
-repartition-type : 0
-bloom : neighbor
-debloom : cascading
-debloom-impl : minimizer
-branching-nodes : stored
-topology-stats : 0
-mphf : emphf
-verbose : 1
-integer-precision : 0
-verbose : 1
stats
traversal : contig
start_selector : best
nb_contigs : 8044789
nb_small_contigs_discarded : 9241683
nt_assembled : 1160242262
max_length : 5239
max_length_left : 4197
max_length_right : 4855
debugging traversal stats
large breadth : 1344
large depth : 135
marked kmer inside traversal : 5595051
traversal ends with dead-ends : 2587076
in-branching large depth : 2178233
in-branching large breadth : 2196283
in-branching other : 3276932
couldn't validate consensuses : 154210
time : 36742.777
assembly : 36742.777
and
[sr320@mox1 0901b]$ ls
AD002_S9_L001_R2_001.contigs.fa slurm-71843.out slurm-71844.out
[sr320@mox1 0901b]$ head AD002_S9_L001_R2_001.contigs.fa
>0__len__91
AAAAAAAAAAAAAAAAAAAAAAAAAACCTCACAAGCTTTGACATATTAATGTTACACTTATTGGTGTACTTAAAAGAAATTACTAGTATAC
>1__len__126
AAAAAAAAAAAAAAAAAAAAAAAAAAACTGCCAGCCAATTAACACAAATTTATAAAATATAATCAGTGACTTAATACATGGGATAGATACGGTGACATTAAGGGATGTGTATTCAGAGCTGTCAAT
>2__len__461
AAAAAAAAAAAAAAAAAAAAAAAAAACGATTTCAGATTGAAATGTAAATATGTTAAGATGCAGCATATTATTTCACATCAACATAAGGTCAAACCTTTGGCAGGTTCGACATGATGATTAATCAAAATATGTTTTGAAATGTATATATACAGGTAACATTGGGTTTATATATATAAACATAATTAAACCCAATGTTGTTGTCTGAAATTCCGGGACTTAGATAAAACAAAAGTTGTATATTTTCCACAGTGAACTATGGTAAAATGGTAAAAACATACATCTTTCTTATTCTTACAGTCCATGGTTGGATTTCTCCATCTTCTTCAAATGGAAATAGAATATATCGTCCTTTTAAAAGTATTATCCTGTACTTTTACAAATCAGACACAATTCATACTTCCGCTCGTCCTCGGTAACAGTTCTTTGTAATAGTGTTACTACTGTCCTTCCTAAAAAAGAAA
>3__len__84
AAAAAAAAAAAAAAAAAAAAAAAAAACGTTGACAAATATGAAAGCAGCATTTTTTCAAATAAAAGCACTGTTTGTCTAGTTAAA
>4__len__101
AAAAAAAAAAAAAAAAAAAAAAAAAATCGGAAAAATACTAATTTCGAAAATTAAAAGGAATGTTAAGGGGCGTGTTAGTTATAACAGCGGAAAAGGTTTCT
Written on September 1, 2017