From 6fd67ae20936547a25258ce82720dac01c4d73a3 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 10 Aug 2022 13:44:57 +0200 Subject: [PATCH 1/2] spades: add OMP_THREAD_LIMIT despite the `-t` argument spades may run only sequential. you find in the logs: ``` Maximum # of threads to use (adjusted due to OMP capabilities): 1 ``` --- tools/spades/biosyntheticspades.xml | 1 + tools/spades/coronaspades.xml | 1 + tools/spades/macros.xml | 5 ++++- tools/spades/metaplasmidspades.xml | 1 + tools/spades/metaspades.xml | 1 + tools/spades/metaviralspades.xml | 1 + tools/spades/plasmidspades.xml | 1 + tools/spades/rnaspades.xml | 2 +- tools/spades/rnaviralspades.xml | 1 + tools/spades/spades.xml | 1 + 10 files changed, 13 insertions(+), 2 deletions(-) diff --git a/tools/spades/biosyntheticspades.xml b/tools/spades/biosyntheticspades.xml index 2aadc91878a..17e730c23de 100644 --- a/tools/spades/biosyntheticspades.xml +++ b/tools/spades/biosyntheticspades.xml @@ -16,6 +16,7 @@ #end if @PREPROCESS_NANOPORE_PACBIO_FILES@ +@OMP_THREADS@ ## run spades.py --bio -o 'output' diff --git a/tools/spades/coronaspades.xml b/tools/spades/coronaspades.xml index 60a9d4dd7af..f75286efbc6 100644 --- a/tools/spades/coronaspades.xml +++ b/tools/spades/coronaspades.xml @@ -19,6 +19,7 @@ @PREPROCESS_SANGER_FILES@ +@OMP_THREADS@ ## run coronaspades.py -o 'output' diff --git a/tools/spades/macros.xml b/tools/spades/macros.xml index f5b31fae725..e6e31fcfcb1 100644 --- a/tools/spades/macros.xml +++ b/tools/spades/macros.xml @@ -1,6 +1,6 @@ 3.15.4 - 1 + 2 spades @@ -43,6 +43,9 @@ + diff --git a/tools/spades/metaplasmidspades.xml b/tools/spades/metaplasmidspades.xml index 7ffc41264f6..861a38ee3b0 100644 --- a/tools/spades/metaplasmidspades.xml +++ b/tools/spades/metaplasmidspades.xml @@ -19,6 +19,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_ASSEMBLY_GRAPH_FILES@ +@OMP_THREADS@ ## run spades.py --meta --plasmid -o 'output' diff --git a/tools/spades/metaspades.xml b/tools/spades/metaspades.xml index 70f8240bff0..c58de118979 100755 --- a/tools/spades/metaspades.xml +++ b/tools/spades/metaspades.xml @@ -16,6 +16,7 @@ #end if @PREPROCESS_NANOPORE_PACBIO_FILES@ +@OMP_THREADS@ ## run metaspades.py -o 'output' diff --git a/tools/spades/metaviralspades.xml b/tools/spades/metaviralspades.xml index a0cb488c6d0..8ccd1479eef 100644 --- a/tools/spades/metaviralspades.xml +++ b/tools/spades/metaviralspades.xml @@ -19,6 +19,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_ASSEMBLY_GRAPH_FILES@ +@OMP_THREADS@ ## run spades.py --metaviral -o 'output' diff --git a/tools/spades/plasmidspades.xml b/tools/spades/plasmidspades.xml index 3685ae9e73d..736af912a25 100644 --- a/tools/spades/plasmidspades.xml +++ b/tools/spades/plasmidspades.xml @@ -19,6 +19,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_ASSEMBLY_GRAPH_FILES@ +@OMP_THREADS@ ## run plasmidspades.py $operation_mode diff --git a/tools/spades/rnaspades.xml b/tools/spades/rnaspades.xml index 3e254ba5883..979aae14f4e 100644 --- a/tools/spades/rnaspades.xml +++ b/tools/spades/rnaspades.xml @@ -18,7 +18,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_FL_RNA_FILES@ - +@OMP_THREADS@ ## run rnaspades.py -o 'output' diff --git a/tools/spades/rnaviralspades.xml b/tools/spades/rnaviralspades.xml index 1a8ccd80e48..12451289813 100644 --- a/tools/spades/rnaviralspades.xml +++ b/tools/spades/rnaviralspades.xml @@ -18,6 +18,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_SANGER_FILES@ +@OMP_THREADS@ ## run spades.py --rnaviral -o 'output' diff --git a/tools/spades/spades.xml b/tools/spades/spades.xml index 7759e818d92..2f23b883bb9 100644 --- a/tools/spades/spades.xml +++ b/tools/spades/spades.xml @@ -18,6 +18,7 @@ @PREPROCESS_CONTIGS_FILES@ @PREPROCESS_SANGER_FILES@ +@OMP_THREADS@ ## run spades.py $operation_mode From 036988a577e66ffc705b58ad7c8e917e7a7b1705 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 10 Aug 2022 14:22:16 +0200 Subject: [PATCH 2/2] spades: remove URL that times out from docs --- tools/spades/biosyntheticspades.xml | 2 +- tools/spades/coronaspades.xml | 2 +- tools/spades/macros.xml | 2 +- tools/spades/metaplasmidspades.xml | 2 +- tools/spades/metaspades.xml | 2 +- tools/spades/metaviralspades.xml | 2 +- tools/spades/plasmidspades.xml | 2 +- tools/spades/rnaspades.xml | 2 +- tools/spades/rnaviralspades.xml | 2 +- tools/spades/spades.xml | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/tools/spades/biosyntheticspades.xml b/tools/spades/biosyntheticspades.xml index 17e730c23de..46c5c7e2e9c 100644 --- a/tools/spades/biosyntheticspades.xml +++ b/tools/spades/biosyntheticspades.xml @@ -176,7 +176,7 @@ A detailed description can be found in the `output section `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1101/gr.243477.118 diff --git a/tools/spades/coronaspades.xml b/tools/spades/coronaspades.xml index f75286efbc6..d670a74112e 100644 --- a/tools/spades/coronaspades.xml +++ b/tools/spades/coronaspades.xml @@ -163,7 +163,7 @@ Input data can be provided as interlaced, forward and reverse, merged and unpair **References** -More information can be found on `github `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1093/bioinformatics/btab597 diff --git a/tools/spades/macros.xml b/tools/spades/macros.xml index e6e31fcfcb1..b635f84a742 100644 --- a/tools/spades/macros.xml +++ b/tools/spades/macros.xml @@ -741,7 +741,7 @@ A detailed description can be found in the `input section `_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o . Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions. +The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our `recommendation for long reads `_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o . Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions. You may need no error correction for Hi-Q enzyme at all. However, we suggest trying to assemble your data with and without error correction and select the best variant. diff --git a/tools/spades/metaplasmidspades.xml b/tools/spades/metaplasmidspades.xml index 861a38ee3b0..e232e3c79cd 100644 --- a/tools/spades/metaplasmidspades.xml +++ b/tools/spades/metaplasmidspades.xml @@ -234,7 +234,7 @@ metaplasmidSPAdes is a subtool for assembling plasmids from metagenomic data set **References** -More information can be found on `github `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1101/gr.241299.118 diff --git a/tools/spades/metaspades.xml b/tools/spades/metaspades.xml index c58de118979..af05e559d94 100755 --- a/tools/spades/metaspades.xml +++ b/tools/spades/metaspades.xml @@ -186,7 +186,7 @@ metaSPAdes is a subtool for assembling metagenomic data sets. **References** -More information can be found on `github `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1101/gr.213959.116 diff --git a/tools/spades/metaviralspades.xml b/tools/spades/metaviralspades.xml index 8ccd1479eef..b8819fba75d 100644 --- a/tools/spades/metaviralspades.xml +++ b/tools/spades/metaviralspades.xml @@ -234,7 +234,7 @@ metaplasmidSPAdes is a subtool for assembling plasmids from metagenomic data set **References** -More information can be found on `github `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1101/gr.241299.118 diff --git a/tools/spades/plasmidspades.xml b/tools/spades/plasmidspades.xml index 736af912a25..9b33eb2a654 100644 --- a/tools/spades/plasmidspades.xml +++ b/tools/spades/plasmidspades.xml @@ -378,7 +378,7 @@ plasmidSPAdes is a subtool for assembling plasmid data sets. **References** -More information can be found on `github `_ and on the `project website `_. +More information can be found on `github `_. ]]> 10.1093/bioinformatics/btw493 diff --git a/tools/spades/rnaspades.xml b/tools/spades/rnaspades.xml index 979aae14f4e..79fd4937968 100644 --- a/tools/spades/rnaspades.xml +++ b/tools/spades/rnaspades.xml @@ -238,7 +238,7 @@ and strand-specificity. Transcript quantification for each sample can be done af **References** -More information can be found on on `github `_ and on the `project website `_. +More information can be found on on `github `_. ]]> 10.1101/420208 diff --git a/tools/spades/rnaviralspades.xml b/tools/spades/rnaviralspades.xml index 12451289813..e6ecb2cb977 100644 --- a/tools/spades/rnaviralspades.xml +++ b/tools/spades/rnaviralspades.xml @@ -352,7 +352,7 @@ rnaviralSPAdes is a pipeline specially designed for de novo assembler tailored f **References** -More information are available on `github `_ and on the `project website `_. +More information are available on `github `_. ]]> diff --git a/tools/spades/spades.xml b/tools/spades/spades.xml index 2f23b883bb9..23bb09761a5 100644 --- a/tools/spades/spades.xml +++ b/tools/spades/spades.xml @@ -732,7 +732,7 @@ spades.py **References** -More information are available on `github `_ and on the `project website `_. +More information are available on `github `_. ]]> 10.1089/cmb.2012.0021