update DBs using RFAM 15.9 & SILVA 138.1

LICENSE.SILVA

@@ -3,35 +3,22 @@ http://www.arb-silva.de/silva-license-information/
 
 SILVA Terms of Use/License Information
 
-The SILVA database content offered at www.arb-silva.de can be freely browsed
-and the corresponding information deployed by all users, independent from
-their status (academic or non-academic).
-
-All downloads are free for academic users. They can be used, modified and
-redistributed within the academic environment without any limitation.
-However, in case of redistribution please make transparent the SILVA Terms
-of Use/License Information by linking/referring to this page (see link in
-the header of your browser). Academic users are represented by universities
-and non-commercial research institutes such as members of the German
-Helmholtz Association, Leibniz Association and Max-Planck Society as well as
-US National Labs.
-
-Users from NON-ACADEMIC can also directly access all downloads including the
-results of the SILVA web-aligner (SINA) but only for limited/temporary use
-(only for test purposes). All downloaded files should be deleted latest
-after 48 hours. Unauthorized usage beyond test purposes is strictly
-prohibited. If you are interested in unlimited usage of the SILVA
-databases/services (e.g. the web-aligner) or parts of them within a
-non-academic environment, please contact us for more information at
-contact(at)arb-silva.de. A non-academic environment is defined by a direct
-or indirect commercial interest in the data and includes all industrial
-research entities.
-
-July 2012
+As of release 138 the SILVA databases, its taxonomy, and all files provided for
+download are licensed unter Creative Commons Attribution 4.0 (CC-BY 4.0).
+
+All data is freely available for academic and commercial use as long as SILVA
+is credited as original author and a link to the full license is provided.
+
+The full license is available:
+    https://creativecommons.org/licenses/by/4.0/ and
+    https://creativecommons.org/licenses/by/4.0/legalcode
 
 Citations
 
-Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J,
-Gloeckner FO (2013) The SILVA ribosomal RNA gene database project: improved
-data processing and web-based tools. Opens external link in new windowNucl.
-Acids Res. 41 (D1): D590-D596.
+If you find SILVA a useful resource for your research or applications please cite:
+
+Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids Res. 41 (D1): D590-D596. http://nar.oxfordjournals.org/content/41/D1/D590
+
+Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO (2014) The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucl. Acids Res. 42:D643-D648 http://nar.oxfordjournals.org/content/42/D1/D643.full
+
+Glöckner FO, Yilmaz P, Quast C, Gerken J, Beccati A, Ciuprina A, Bruns G, Yarza P, Peplies J, Westram R, Ludwig W (2017) 25 years of serving the community with ribosomal RNA gene reference databases and tools. J. Biotechnol. http://www.sciencedirect.com/science/article/pii/S0168165617314943

README.md

@@ -173,7 +173,7 @@ by Torsten Seemann and Tim Booth.
 
 * Barrnap: [GPLv3](https://raw.githubusercontent.com/tseemann/barrnap/master/LICENSE)
 * Rfam: [CC0](https://raw.githubusercontent.com/tseemann/barrnap/master/LICENSE.Rfam)
-* SILVA: [Free for academic use](https://raw.githubusercontent.com/tseemann/barrnap/master/LICENSE.SILVA)
+* SILVA: [Creative Commons Attribution 4.0 (CC-BY 4.0](https://www.arb-silva.de/silva-license-information/)
 
 ## Author
 

build/build_HMMs.sh

@@ -1,24 +1,26 @@
 #!/bin/bash
 
-CPUS=$(grep -c bogomips /proc/cpuinfo)
+CPUS=$(nproc)
 CURL="curl"
-GUNZIP="gzip -c"
+GUNZIP="gunzip"
 
 RFAM="Rfam.seed"
-RFAMURL="ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/${RFAM}.gz"
+RFAMURL="https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/${RFAM}.gz"
+# RFAM 14.9 as of 2023-09-16
 if [ ! -r "$RFAM" ]; then
   echo "Downloading: $RFAM"
-  $CURL "$RFAMURL" | $GUNZIP -c > "$RFAM"
+  $CURL "$RFAMURL" | $GUNZIP -c - > "$RFAM"
 else
   echo "Using existing file: $RFAM"
 fi
 
+# https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/SILVA_138.1_LSURef_tax_silva_full_align_trunc.fasta.gz
 # 23S only as 16S is in RFAM
-SILVA="SILVA_128_LSURef_tax_silva_full_align_trunc.fasta"
-SILVAURL="http://www.arb-silva.de/fileadmin/silva_databases/current/Exports/${SILVA}.gz"
+SILVA="SILVA_138.1_LSURef_tax_silva_full_align_trunc.fasta"
+SILVAURL="https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/${SILVA}.gz"
 if [ ! -r "$SILVA" ]; then
   echo "Downloading: $SILVA"
-  $CURL "$SILVAURL" | $GUNZIP -c > "$SILVA"
+  $CURL "$SILVAURL" | $GUNZIP -c - > "$SILVA"
 else
   echo "Using existing file: $SILVA"
 fi