Skip to content

GitLab

Commit fb67be9f authored by peguerin's avatar peguerin
Browse files

Initial commit

parents
Expand all Hide whitespace changes
Inline Side-by-side
README.md 0 → 100644
View file @ fb67be9f
main folder
pedir
180802_NB501473_A_L1-4_ANIZ-1_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
180802_NB501473_A_L1-4_ANIZ-1_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
180802_NB501473_A_L1-4_ANIZ-2_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
180802_NB501473_A_L1-4_ANIZ-2_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
medir
180806_NB501850_A_L1-4_ANIZ-3_R1.fastq
180806_NB501850_A_L1-4_ANIZ-3_R2.fastq
180807_NB501850_A_L1-4_ANIZ-4_R1.fastq
180807_NB501850_A_L1-4_ANIZ-4_R2.fastq
xdir
Lib_10_S1_L002_I1_001.fastq
Lib_10_S1_L002_R1_001.fastq
Lib_10_S1_L002_R2_001.fastq
xxx
arcs/download.sh 0 → 100644
View file @ fb67be9f
## download files
## sur MARBEC /media/superdisk/reservebenefit/donnees/genomes
scp serran_genome_lgt3000.fasta peguerin@162.38.181.163:/media/bigvol/peguerin/donnees/
## sur MBB /share/reservebenefit/RAW/RESERVEBENEFIT/whole_genome_sequencing/wgs_serran/10Xgenomics
scp * peguerin@162.38.181.163:/media/bigvol/peguerin/donnees/
mkdir ~/donnees/lib10x
cd ~/donnees/
mv Lib_*gz lib10x/
arcs/install.sh 0 → 100644
View file @ fb67be9f
sudo apt-get -y --force-yes update
sudo apt-get install --reinstall zlibc zlib1g zlib1g-dev
sudo apt-get install autotools-dev
yes | sudo apt-get install automake
sudo apt install wget
yes | sudo apt-get install libboost-all-dev
wget http://www.bcgsc.ca/platform/bioinfo/software/links/releases/1.8.6/links_v1-8-6.tar.gz
gunzip links_v1-8-6.tar.gz
tar -xvf links_v1-8-6.tar
sudo echo "en_US.UTF-8 UTF-8" > /etc/locale.gen
sudo echo "fr_FR.UTF-8 UTF-8" >> /etc/locale.gen
sudo locale-gen
git clone https://github.com/bcgsc/arcs.git
cd arcs
./autogen.sh
./configure
make
sudo make install
cd ..
echo "export PATH=$PATH:/media/bigvol/peguerin/links_v1.8.6/" >> ~/.bashrc
## install longranger
wget -O longranger-2.2.2.tar.gz "http://cf.10xgenomics.com/releases/genome/longranger-2.2.2.tar.gz?Expires=1554242254&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9nZW5vbWUvbG9uZ3Jhbmdlci0yLjIuMi50YXIuZ3oiLCJDb25kaXRpb24iOnsiRGF0ZUxlc3NUaGFuIjp7IkFXUzpFcG9jaFRpbWUiOjE1NTQyNDIyNTR9fX1dfQ__&Signature=CWpdq48GhG9gCSvSYHSJcJWUMSBuw7h58tsdyDB~FqIf5ktXVJr4kN2t3ycjz9aTCtJ961d3dVyGMgiGxATtqO-ajEa0zNEihxf1nWMPxHMkLEZDo7-OO28MaJoXFsfo8a91PVVBL7UraVdHZ8ijdUG75wkoONHIo~VBX-OrdDY3RwtBLAc1AwB3sfOClw2~u5z-rGW8YeC49Vim8WHwzyK1Xp6ybAuqV9~mOEChLHNtYqmqIihmSFPoFWXtO7Lm~YCD~j-zg16xtiPWBQrvrlXuxd2V185MtraMrsxAm5Zd7FoypgjuNsFU3qo1PqznNbrPao8OOXZXZV8gcU10gw__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"
tar -xzvf longranger-2.2.2.tar.gz
longranger testrun --id=tiny
echo "export PATH=$PATH:/media/bigvol/peguerin/longranger-2.2.2/" >> ~/.bashrc
## install Tigmint
sudo apt-get install bedtools bwa samtools
sudo apt-get install seqtk abyss
sudo apt install python3-pip
pip3 install intervaltree pybedtools pysam statistics
git clone https://github.com/bcgsc/tigmint
echo "export PATH=$PATH:/media/bigvol/peguerin/tigmint/bin" >> ~/.bashrc
brew tap brewsci/bio
wget http://www.bcgsc.ca/downloads/supplementary/ARCS/testdata/links_c5r0.05e30000-l5-a0.9.scaffolds.fa
\ No newline at end of file
arcs/pipeline.sh 0 → 100644
View file @ fb67be9f
## produce interleaved filefastq from 10X raw data
longranger basic --fastqs=/media/bigvol/peguerin/donnees/lib10x/ --id=xxx --sample=Lib_10
platanus/sar/SLURM_sar_assembly_gapclose.job 0 → 100755
View file @ fb67be9f
#!/bin/bash
#SBATCH --job-name=sar_gapclose
#SBATCH --account=reservebenefit
#SBATCH --partition=thau-smp
#SBATCH --mail-user=pierre-edouard.guerin@cefe.cnrs.fr
#SBATCH -n 1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=80
#SBATCH --mem 1024000
module purge
module load cv-standard
module load intel/compiler/64/2016.3.210
export OMP_NUM_THREADS=80
/nfs/work/reservebenefit/bin/platanus gap_close -t 80 -tmp /nfsthau/sar_temp -o sar_hpc_g -c /nfs/work/reservebenefit/sar_working/sar_hpc_scaffold.fa -IP1 /nfs/work/reservebenefit/sar_raw_data/paired/goodlength_goodqual_170106_SNK268_A_L006_GWM-869_R1.fastq /nfs/work/reservebenefit/sar_raw_data/paired/goodlength_goodqual_170106_SNK268_A_L006_GWM-869_R2.fastq -IP2 /nfs/work/reservebenefit/sar_raw_data/paired/goodlength_goodqual_170106_SNK268_A_L007_GWM-870_R1.fastq /nfs/work/reservebenefit/sar_raw_data/paired/goodlength_goodqual_170106_SNK268_A_L007_GWM-870_R2.fastq -OP3 /nfs/work/reservebenefit/sar_raw_data/mate_pair/goodqual_170106_SNK268_A_L008_GWM-871_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq /nfs/work/reservebenefit/sar_raw_data/mate_pair/goodqual_170106_SNK268_A_L008_GWM-871_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq -OP4 /nfs/work/reservebenefit/sar_raw_data/mate_pair/goodqual_170106_SNK268_A_L008_GWM-872_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq /nfs/work/reservebenefit/sar_raw_data/mate_pair/goodqual_170106_SNK268_A_L008_GWM-872_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq 2> gapclose.log
platanus/serran/log/serran_mbb_assemble.log 0 → 100755
View file @ fb67be9f
Platanus version: 1.2.4
/media/bigvol/peguerin/programmes/platanus assemble -tmp /media/bigvol/peguerin/temp/ -m 256 -t 64 -o serran_assemble -f /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180806_NB501850_A_L1-4_ANIZ-3_R1.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180806_NB501850_A_L1-4_ANIZ-3_R2.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180807_NB501850_A_L1-4_ANIZ-4_R1.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180807_NB501850_A_L1-4_ANIZ-4_R2.fastq
K = 32, saving kmers from reads...
AVE_READ_LEN=150
KMER_EXTENSION:
K=32, KMER_COVERAGE=187.5 (>= 47), COVERAGE_CUTOFF=47
K=42, KMER_COVERAGE=171.743, COVERAGE_CUTOFF=47, PROB_SPLIT=10e-inf
K=52, KMER_COVERAGE=155.987, COVERAGE_CUTOFF=47, PROB_SPLIT=10e-inf
K=62, KMER_COVERAGE=140.231, COVERAGE_CUTOFF=47, PROB_SPLIT=10e-inf
K=72, KMER_COVERAGE=124.474, COVERAGE_CUTOFF=47, PROB_SPLIT=10e-14.1837
K=82, KMER_COVERAGE=108.718, COVERAGE_CUTOFF=47, PROB_SPLIT=10e-10.0109
K=92, KMER_COVERAGE=92.9619, COVERAGE_CUTOFF=36, PROB_SPLIT=10e-10.2541
K=102, KMER_COVERAGE=77.2057, COVERAGE_CUTOFF=26, PROB_SPLIT=10e-10.3219
K=112, KMER_COVERAGE=61.4494, COVERAGE_CUTOFF=17, PROB_SPLIT=10e-10.2223
K=122, KMER_COVERAGE=45.6932, COVERAGE_CUTOFF=9, PROB_SPLIT=10e-10.0483
K=130, KMER_COVERAGE=33.0882, COVERAGE_CUTOFF=3, PROB_SPLIT=10e-10.6512
K=133, KMER_COVERAGE=28.3613, COVERAGE_CUTOFF=2, PROB_SPLIT=10e-10.2473
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=651542
NUM_CUT=4701
NUM_CUT=13
NUM_CUT=0
TOTAL_NUM_CUT=656256
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=1001924409
TOTAL_UNMAPPED_READS=509379943
TOTAL_SHORT_READS(<32)=0
NUM_DELETE_NODE(reads are unmapped)=1702783
NUM_CUT_NODE=199148
extracting reads (containing kmer used in contig assemble)...
K = 42, loading kmers from contigs...
K = 42, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 47
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=408722
NUM_CUT=3994
NUM_CUT=12
NUM_CUT=1
NUM_CUT=0
TOTAL_NUM_CUT=412729
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=995588437
TOTAL_UNMAPPED_READS=515715915
TOTAL_SHORT_READS(<42)=0
NUM_DELETE_NODE(reads are unmapped)=1001592
NUM_CUT_NODE=183125
extracting reads (containing kmer used in contig assemble)...
K = 52, loading kmers from contigs...
K = 52, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 47
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=285064
NUM_CUT=3101
NUM_CUT=17
NUM_CUT=0
TOTAL_NUM_CUT=288182
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=990692965
TOTAL_UNMAPPED_READS=520611387
TOTAL_SHORT_READS(<52)=0
NUM_DELETE_NODE(reads are unmapped)=635802
NUM_CUT_NODE=141747
extracting reads (containing kmer used in contig assemble)...
K = 62, loading kmers from contigs...
K = 62, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 47
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=208668
NUM_CUT=2331
NUM_CUT=14
NUM_CUT=0
TOTAL_NUM_CUT=211013
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=985497264
TOTAL_UNMAPPED_READS=525807088
TOTAL_SHORT_READS(<62)=0
NUM_DELETE_NODE(reads are unmapped)=428937
NUM_CUT_NODE=118181
extracting reads (containing kmer used in contig assemble)...
K = 72, loading kmers from contigs...
K = 72, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 47
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=153902
NUM_CUT=1847
NUM_CUT=19
NUM_CUT=0
TOTAL_NUM_CUT=155768
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=976217974
TOTAL_UNMAPPED_READS=535086378
TOTAL_SHORT_READS(<72)=0
NUM_DELETE_NODE(reads are unmapped)=274392
NUM_CUT_NODE=115979
extracting reads (containing kmer used in contig assemble)...
K = 82, loading kmers from contigs...
K = 82, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 47
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=119454
NUM_CUT=1363
NUM_CUT=19
NUM_CUT=1
NUM_CUT=0
TOTAL_NUM_CUT=120837
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=956250530
TOTAL_UNMAPPED_READS=555053822
TOTAL_SHORT_READS(<82)=0
NUM_DELETE_NODE(reads are unmapped)=170679
NUM_CUT_NODE=140994
extracting reads (containing kmer used in contig assemble)...
K = 92, loading kmers from contigs...
K = 92, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 36
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=127345
NUM_CUT=1358
NUM_CUT=20
NUM_CUT=1
NUM_CUT=0
TOTAL_NUM_CUT=128724
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=956281893
TOTAL_UNMAPPED_READS=555022459
TOTAL_SHORT_READS(<92)=0
NUM_DELETE_NODE(reads are unmapped)=202240
NUM_CUT_NODE=101230
extracting reads (containing kmer used in contig assemble)...
K = 102, loading kmers from contigs...
K = 102, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 26
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=143251
NUM_CUT=1538
NUM_CUT=18
NUM_CUT=0
TOTAL_NUM_CUT=144807
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=957690090
TOTAL_UNMAPPED_READS=553614262
TOTAL_SHORT_READS(<102)=0
NUM_DELETE_NODE(reads are unmapped)=201591
NUM_CUT_NODE=98938
extracting reads (containing kmer used in contig assemble)...
K = 112, loading kmers from contigs...
K = 112, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 17
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=171872
NUM_CUT=1935
NUM_CUT=31
NUM_CUT=0
TOTAL_NUM_CUT=173838
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=960004902
TOTAL_UNMAPPED_READS=551299450
TOTAL_SHORT_READS(<112)=0
NUM_DELETE_NODE(reads are unmapped)=197690
NUM_CUT_NODE=104598
extracting reads (containing kmer used in contig assemble)...
K = 122, loading kmers from contigs...
K = 122, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 9
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=239781
NUM_CUT=3058
NUM_CUT=36
NUM_CUT=1
NUM_CUT=0
TOTAL_NUM_CUT=242876
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=962809341
TOTAL_UNMAPPED_READS=548495011
TOTAL_SHORT_READS(<122)=0
NUM_DELETE_NODE(reads are unmapped)=201309
NUM_CUT_NODE=120265
extracting reads (containing kmer used in contig assemble)...
K = 130, loading kmers from contigs...
K = 130, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 3
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=750698
NUM_CUT=12437
NUM_CUT=158
NUM_CUT=5
NUM_CUT=1
NUM_CUT=0
TOTAL_NUM_CUT=763299
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=966236990
TOTAL_UNMAPPED_READS=545067362
TOTAL_SHORT_READS(<130)=0
NUM_DELETE_NODE(reads are unmapped)=352054
NUM_CUT_NODE=162080
extracting reads (containing kmer used in contig assemble)...
K = 133, loading kmers from contigs...
K = 133, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 2
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=1012616
NUM_CUT=17404
NUM_CUT=157
NUM_CUT=3
NUM_CUT=0
TOTAL_NUM_CUT=1030180
LENGTH_CUTOFF = 266
COVERAGE_CUTOFF = 2
removing erroneous nodes...
NUM_REMOVED_NODES=0
TOTAL_NUM_REMOVED_NODES=0
AVE_KMER_COV_REMOVING_BUBBLE=33.8625
removing bubbles...
BUBBLE_IDENTITY_THRESHOLD=0.1
NUM_REMOVED_BUBBLES=674748
NUM_REMOVED_BUBBLES=17
NUM_REMOVED_BUBBLES=0
TOTAL_NUM_REMOVED_BUBBLES=674765
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=817267252
TOTAL_UNMAPPED_READS=694037100
TOTAL_SHORT_READS(<133)=0
NUM_DELETE_NODE(reads are unmapped)=243922
NUM_CUT_NODE=174957
assemble completed!
#### PROCESS INFORMATION ####
VmPeak: 271.401 GByte
VmHWM: 77.592 GByte
platanus/serran/log/serran_mbb_gapclose.log 0 → 100644
View file @ fb67be9f
Platanus version: 1.2.4
/media/bigvol/peguerin/programmes/platanus gap_close -t 80 -tmp /media/bigvol/peguerin/temp/ -o serran_hpc_gapclose -c /media/bigvol/peguerin/out_scaffold.fa -IP1 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180806_NB501850_A_L1-4_ANIZ-3_R1.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180806_NB501850_A_L1-4_ANIZ-3_R2.fastq -IP2 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180807_NB501850_A_L1-4_ANIZ-4_R1.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180807_NB501850_A_L1-4_ANIZ-4_R2.fastq -OP3 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-1_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-1_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq -OP4 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-2_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-2_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
K=32, making hash table...
[PAIR_LIBRARY 1]
mapping reads...
TOTAL_PAIR = 532907809
MAPPED_IN_SAME_CONTIG = 382797092 (0.718318)
estimating insert-size...
PEAK = 297
LOWER_LIMIT (permissible range to estimate AVE_INS)= 74
UPPER_LIMIT (permissible range to estimate AVE_INS)= 520
AVE_INS = 291
SD_INS = 46
mapping reads that cover small gaps...
[PAIR_LIBRARY 2]
mapping reads...
TOTAL_PAIR = 222744367
MAPPED_IN_SAME_CONTIG = 125736962 (0.56449)
estimating insert-size...
PEAK = 502
LOWER_LIMIT (permissible range to estimate AVE_INS)= 126
UPPER_LIMIT (permissible range to estimate AVE_INS)= 879
AVE_INS = 394
SD_INS = 136
mapping reads that cover small gaps...
[PAIR_LIBRARY 3]
mapping reads...
TOTAL_PAIR = 111002624
MAPPED_IN_SAME_CONTIG = 65215058 (0.587509)
estimating insert-size...
PEAK = 2721
LOWER_LIMIT (permissible range to estimate AVE_INS)= 680
UPPER_LIMIT (permissible range to estimate AVE_INS)= 4762
AVE_INS = 2883
SD_INS = 467
mapping reads that cover small gaps...
[PAIR_LIBRARY 4]
mapping reads...
TOTAL_PAIR = 45010713
MAPPED_IN_SAME_CONTIG = 23215702 (0.515782)
estimating insert-size...
PEAK = 5371
LOWER_LIMIT (permissible range to estimate AVE_INS)= 1343
UPPER_LIMIT (permissible range to estimate AVE_INS)= 9399
AVE_INS = 5200
SD_INS = 1094
mapping reads that cover small gaps...
making hash table of gaps...
making consensus sequences to close small gaps...
NUM_GAP=135782
NUM_CLOSED_GAP=23659
[PAIR_LIBRARY 1]
saving reads covering gaps...
loading reads covering gaps...
assembling localized reads...
NUM_GAPS = 112123
NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 126
NUM_CLOSED_GAPS_USING_DE_BRUIJN = 27732
NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 8166
[PAIR_LIBRARY 2]
saving reads covering gaps...
loading reads covering gaps...
assembling localized reads...
NUM_GAPS = 76225
NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 135
NUM_CLOSED_GAPS_USING_DE_BRUIJN = 8606
NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 5414
[PAIR_LIBRARY 3]
saving reads covering gaps...
loading reads covering gaps...
assembling localized reads...
NUM_GAPS = 62205
NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 8
NUM_CLOSED_GAPS_USING_DE_BRUIJN = 778
NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 2858
[PAIR_LIBRARY 4]
saving reads covering gaps...
loading reads covering gaps...
assembling localized reads...
NUM_GAPS = 58569
NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 31
NUM_CLOSED_GAPS_USING_DE_BRUIJN = 8
NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 262
[ALL LIBRARY]
assembling localized reads...
NUM_GAPS = 58299
NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 192
NUM_CLOSED_GAPS_USING_DE_BRUIJN = 1283
NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 428
TOTAL_NUM_CLOSED_GAPS = 79194
gap_close completed!!
#### PROCESS INFORMATION ####
VmPeak: 48.887 GByte
VmHWM: 5.191 GByte
platanus/serran/log/serran_mbb_scaffold.log 0 → 100644
View file @ fb67be9f
This diff is collapsed.
platanus/serran/scripts/run_platanus_contig.sh 0 → 100755
View file @ fb67be9f
/media/bigvol/peguerin/programmes/platanus assemble -tmp /media/bigvol/peguerin/temp/ -m 256 -t 64 -o serran_assemble -f /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180806_NB501850_A_L1-4_ANIZ-3_R1.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180806_NB501850_A_L1-4_ANIZ-3_R2.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180807_NB501850_A_L1-4_ANIZ-4_R1.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180807_NB501850_A_L1-4_ANIZ-4_R2.fastq 2> assemble.log
platanus/serran/scripts/run_platanus_gapclose.sh 0 → 100644
View file @ fb67be9f
/media/bigvol/peguerin/programmes/platanus gap_close -t 80 -tmp /media/bigvol/peguerin/temp/ -o serran_hpc_gapclose -c /media/bigvol/peguerin/out_scaffold.fa -IP1 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180806_NB501850_A_L1-4_ANIZ-3_R1.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180806_NB501850_A_L1-4_ANIZ-3_R2.fastq -IP2 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180807_NB501850_A_L1-4_ANIZ-4_R1.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180807_NB501850_A_L1-4_ANIZ-4_R2.fastq -OP3 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-1_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-1_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq -OP4 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-2_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-2_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq 2> gapclose.log
platanus/serran/scripts/run_platanus_scaffold.sh 0 → 100644
View file @ fb67be9f
/media/bigvol/peguerin/programmes/platanus scaffold -t 80 -tmp /media/bigvol/peguerin/temp/ -c /media/bigvol/peguerin/serran_assemble_contig.fa -b /media/bigvol/peguerin/serran_assemble_contigBubble.fa -IP1 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180806_NB501850_A_L1-4_ANIZ-3_R1.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180806_NB501850_A_L1-4_ANIZ-3_R2.fastq -IP2 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180807_NB501850_A_L1-4_ANIZ-4_R1.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-3-4/data/180807_NB501850_A_L1-4_ANIZ-4_R2.fastq -OP3 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-1_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-1_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq -OP4 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-2_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-2_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq 2> scaffold.log
platanus_alle_10X/assemble.sh 0 → 100644
View file @ fb67be9f
### download longranger
#wget -O longranger-2.2.2.tar.gz "http://cf.10xgenomics.com/releases/genome/longranger-2.2.2.tar.gz?Expires=1547519178&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9nZW5vbWUvbG9uZ3Jhbmdlci0yLjIuMi50YXIuZ3oiLCJDb25kaXRpb24iOnsiRGF0ZUxlc3NUaGFuIjp7IkFXUzpFcG9jaFRpbWUiOjE1NDc1MTkxNzh9fX1dfQ__&Signature=Hc44pebGAA9E6Aguhum0gHiuAnko-bxW-gftlHdNqt9mHKEjaIPxHaZLtym8QS4DaYic~LEBbc3p2uyQ7J-cnHhGE5hQDAihJzx3ur2UsTzZmESaEwRo9aTuwrHz34amN0MV~4I-X5-862-cfkZZfqy-c3N0tgB8lwRc0v1IZc1ULwVoNGLiMosxNgwMLlDzxU69gpugpIKhd-KCJ-v-UIl2inBVrDTTpv9cmj2jY7fabmrCXMmO-Itbi5w4OEGPS7N~KSMBqM8JQ-fHMhMDUNLSWSopMgT-sW6HPRPvWviFyXLMdN~wg8HcQsQTz7FNLn0AhY6YweOvtZtB7TK5ag__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"
###define program path
export PATH=/media/bigvol/peguerin/src/longranger-2.2.2:$PATH
export PATH=/media/bigvol/peguerin/src/Platanus_allee_v2.0.1_Linux_x86_64:$PATH
pe1_R1=/media/bigvol/peguerin/180802_NB501473_A_L1-4_ANIZ-1_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq.gz
pe1_R2=/media/bigvol/peguerin/180802_NB501473_A_L1-4_ANIZ-1_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq.gz
pe2_R1=/media/bigvol/peguerin/180802_NB501473_A_L1-4_ANIZ-2_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq.gz
pe2_R2=/media/bigvol/peguerin/180802_NB501473_A_L1-4_ANIZ-2_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq.gz
platanus_allee assemble -m 256 -t 64 -f $pe1_R1 $pe1_R2 $pe2_R1 $pe2_R2 2>assemble.log
platanus_alle_10X/longranger.sh 0 → 100644
View file @ fb67be9f
export PATH=/media/bigvol/peguerin/src/longranger-2.2.2:$PATH
longranger basic --fastqs=/media/bigvol/peguerin/xdir/ --id=xxx --sample=Lib_10
#gunzip xxx/outs/barcoded.fastq.gz
\ No newline at end of file
platanus_alle_10X/phase.sh 0 → 100644
View file @ fb67be9f
###define program path
export PATH=/media/bigvol/peguerin/src/longranger-2.2.2:$PATH
export PATH=/media/bigvol/peguerin/src/Platanus_allee_v2.0.1_Linux_x86_64:$PATH
pe1_R1=/media/bigvol/peguerin/180802_NB501473_A_L1-4_ANIZ-1_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
pe1_R2=/media/bigvol/peguerin/180802_NB501473_A_L1-4_ANIZ-1_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
pe2_R1=/media/bigvol/peguerin/180802_NB501473_A_L1-4_ANIZ-2_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
pe2_R2=/media/bigvol/peguerin/180802_NB501473_A_L1-4_ANIZ-2_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
mp1_R1=/media/bigvol/peguerin/180806_NB501850_A_L1-4_ANIZ-3_R1.fastq
mp1_R2=/media/bigvol/peguerin/180806_NB501850_A_L1-4_ANIZ-3_R2.fastq
mp2_R1=/media/bigvol/peguerin/180807_NB501850_A_L1-4_ANIZ-4_R1.fastq
mp2_R2=/media/bigvol/peguerin/180807_NB501850_A_L1-4_ANIZ-4_R2.fastq
Xbarcode=/media/bigvol/peguerin/xxx/outs/barcoded.fastq
platanus_allee phase \
-c out_contig.fa out_junctionKmer.fa \
-t 64 \
-IP1 $pe1_R1 $pe1_R2 \
-IP2 $pe2_R1 $pe2_R2 \
-OP3 $mp1_R1 $mp1_R2 \
-OP4 $mp2_R1 $mp2_R2 \
-x $Xbarcode \
2>phase.log
\ No newline at end of file
superstar/mbb_commands.sh 0 → 100755
View file @ fb67be9f
nohup ./programmes/supernova-2.1.1/supernova run --id=serran --fastqs=~/rawdata/ --localmem=470 --maxreads=298666666 &
nohup /media/bigvol/peguerin/programmes/supernova-2.1.1/supernova mkoutput --style=pseudohap2 --asmdir=/media/bigvol/peguerin/serran/outs/assembly --outprefix=serranus &
superstar/serran_assembly_chromium.job 0 → 100755
View file @ fb67be9f
#!/bin/bash
#SBATCH --job-name=serran_assemble
#SBATCH --account=reservebenefit
#SBATCH --partition=thau-smp
#SBATCH --mail-user=pierre-edouard.guerin@cefe.cnrs.fr
#SBATCH -n 1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --mem 1024000
#SBATCH --time=0
module purge
export OMP_NUM_THREADS=64
/nfs/work/reservebenefit/bin/supernova-2.1.1/supernova run --id=serran2 --fastqs=/nfs/work/reservebenefit/serran_raw_data/10X_data/ --maxreads=298666666 --localmem=512
superstar/serran_mkoutput_chromium.job 0 → 100755
View file @ fb67be9f
#!/bin/bash
#SBATCH --job-name=serran_assemble
#SBATCH --account=reservebenefit
#SBATCH --partition=thau-smp
#SBATCH --mail-user=pierre-edouard.guerin@cefe.cnrs.fr
#SBATCH -n 1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --mem 1024000
#SBATCH --time=0
module purge
export OMP_NUM_THREADS=64
/nfs/work/reservebenefit/bin/supernova-2.1.1/supernova mkoutput --style=pseudohap2 --asmdir=/nfs/work/reservebenefit/serran_working/chromium_assembly/serran2/outs/assembly --outprefix=serranus_final
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment