Antonio Fernandez-Guerra genomewalker
genomewalker
/ nonpareil_parser.R
Created
May 18, 2018 11:42
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| library(Nonpareil) | |
| library(tidyverse) | |
| f <- list.files(path="/scratch/antonio/nonpareil/out/", pattern = "npo") | |
| f <- list.files(path="~/tara_nonpareil/", pattern = "npo") | |
| sample.names <- sapply(strsplit(f, ".npo"), `[`, 1) | |
| Nonpareil.curve(f[[1]]) | |
| results_np_tara <- lapply(file.path("~/tara_nonpareil/",f), Nonpareil.curve) |
genomewalker
/ mmseqs_20180926.log
Created
September 26, 2018 08:02
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| Program call: | |
| search QUERY DB results tmp --num-iterations 2 -e 1e-5 -c 0.4 | |
| MMseqs Version: 199d9b81f8cd6af9e66f97ef4dc0bd53c8fce12b | |
| Sub Matrix blosum62.out | |
| Add backtrace true | |
| Alignment mode 2 | |
| E-value threshold 1e-05 | |
| Seq. Id Threshold 0 | |
| Seq. Id. Mode 0 |
genomewalker
/ ifb_core_vm_cpu.txt
Created
September 26, 2018 08:13
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| processor : 0 | |
| vendor_id : GenuineIntel | |
| cpu family : 6 | |
| model : 60 | |
| model name : Intel Core Processor (Haswell, no TSX, IBRS) | |
| stepping : 1 | |
| microcode : 0x1 | |
| cpu MHz : 2294.684 | |
| cache size : 16384 KB | |
| physical id : 0 |
genomewalker
/ get_SOIL_info
Last active
November 29, 2018 18:31
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| cat SRC_sample_ids.txt | parallel -j 16 esearch -db sra -query {} | efetch -format runinfo > stats |
genomewalker
/ pvec.h.patch
Created
December 9, 2018 11:13
Adapted patch from https://github.com/sim82/papara_nt/issues/3
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| --- pvec.h 2018-12-09 12:08:14.727171805 +0100 | |
| +++ pvec_mod.h 2018-12-09 12:09:36.186071505 +0100 | |
| @@ -539,22 +539,26 @@ | |
| static inline double gap_posterior( double v1, double v2 ) { | |
| - assert( pgap_model.is_valid_ptr() ); | |
| - //return v1 / (v1 + v2); | |
| + assert( pgap_model.is_valid_ptr() ); | |
| + //return v1 / (v1 + v2); |
genomewalker
/ create_alluvial.R
Last active
December 10, 2018 09:18
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| #!/usr/bin/env Rscript | |
| args = commandArgs(trailingOnly=TRUE) | |
| # test if there is at least one argument: if not, return an error | |
| if (length(args) == 0) { | |
| stop("At least one argument must be supplied (input file).n", call = FALSE) | |
| } else if (length(args) == 1) { | |
| # default output file | |
| args[2] = "alluvial.tsv" |
genomewalker
/ mmseqs_20190131.log
Created
January 31, 2019 16:21
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| ubuntu@bibigrid-master-64y44t0ith2ejcj:/vol/attached/data/opt/test/MMseqs2/build$ cmake -DHAVE_MPI=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. .. | |
| -- The CXX compiler identification is GNU 5.4.0 | |
| -- The C compiler identification is GNU 5.4.0 | |
| -- Check for working CXX compiler: /usr/bin/c++ | |
| -- Check for working CXX compiler: /usr/bin/c++ -- works | |
| -- Detecting CXX compiler ABI info | |
| -- Detecting CXX compiler ABI info - done | |
| -- Detecting CXX compile features | |
| -- Detecting CXX compile features - done | |
| -- Check for working C compiler: /usr/bin/cc |
genomewalker
/ annotate_query_sequences.R
Last active
March 29, 2019 06:51
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| #!/usr/bin/env Rscript | |
| # Check if basic packages are installed ----------------------------------- | |
| is.installed <- function(pkg){ | |
| is.element(pkg, installed.packages()[,1]) | |
| } | |
| if (!is.installed("crayon") || !is.installed("optparse")){ | |
| cat("We will try to install the packages crayon and optparse... (this will be only be done once)\n") |
genomewalker
/ clusterupdate_7-4e23d.log
Created
April 29, 2019 20:16
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| + set -e | |
| + MMSEQS=/vol/attached/opt/MMseqs2-7-4e23d/bin/mmseqs | |
| + DIR=/vol/attached/gtdb | |
| + SDIR=/vol/scratch/gtdb | |
| + export 'OMPI_MCA_btl=^openib' | |
| + OMPI_MCA_btl='^openib' | |
| + export OMP_NUM_THREADS=28 | |
| + OMP_NUM_THREADS=28 | |
| + RUNNER='mpirun --mca btl_tcp_if_include ens3 -n 10 --map-by ppr:1:node --bind-to none ' | |
| + /vol/attached/opt/MMseqs2-7-4e23d/bin/mmseqs clusterupdate /vol/scratch/gtdb/marine_hmp_db_03112017 /vol/scratch/gtdb/mg_gtdb_orfs_db /vol/scratch/gtdb/marine_hmp_db_03112017_clu /vol/attached/gtdb/mg_gtdb_update/mg_gtdb_db_052019 /vol/attached/gtdb/mg_gtdb_update/mg_gtdb_db_ |
genomewalker
/ clusterupdate_39ee37f97ab065a3763ee10b834b3e6e25aae491.log
Created
April 29, 2019 20:19
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| + set -e | |
| + MMSEQS=/vol/attached/opt/MPI/MMseqs2/bin/mmseqs | |
| + DIR=/vol/attached/gtdb | |
| + SDIR=/vol/scratch/gtdb | |
| + export 'OMPI_MCA_btl=^openib' | |
| + OMPI_MCA_btl='^openib' | |
| + export OMP_NUM_THREADS=28 | |
| + OMP_NUM_THREADS=28 | |
| + RUNNER='mpirun --mca btl_tcp_if_include ens3 -n 10 --map-by ppr:1:node --bind-to none ' | |
| + /vol/attached/opt/MPI/MMseqs2/bin/mmseqs clusterupdate /vol/scratch/gtdb/marine_hmp_db_03112017 /vol/scratch/gtdb/mg_gtdb_orfs_db /vol/scratch/gtdb/marine_hmp_db_03112017_clu /vol/attached/gtdb/mg_gtdb_update/mg_gtdb_db_052019 /vol/attached/gtdb/mg_gtdb_update/mg_gtdb_db_0520 |