search

nselem / corason

Bioinformatic Tools for study Evolution of metabolic diversity
GNU Affero General Public License v3.0
28 stars 12 forks source link

Corason (BiG-SCAPE) issues #14

Open Molyneux12321 opened 2 months ago

Molyneux12321 commented 2 months ago

Hi,

Attempting to use Corason within the "tutorial" from BiG-SCAPE/Corason site using TauD and selected genomes (https://bigscape-corason.secondarymetabolites.org/tutorial/), on a Windows 11 Operating System within the WSL Linux command prompt. No SVG file has been made after this run- can't work out where the issue is, any help appreciated!

$ ~/bin/run_corason ~/bin/example2/TauD2.fasta ~/bin/example2/gbks/gbks ~/bin/example2/gbks/gbks/JM GX01000001.1.cluster003.gbk \

--g

corason is now running docker run --volume /home/molyneux321/bin/example2/TauD2.fasta:/home/output/TauD2.fasta:ro --volume /home/molyneux321/bin/example2/gbks/gbks:/home/output/CORASON_GENOMES:ro --volume /home/molyneux321:/home/output:rw --detach=false --rm nselem/corason corason.pl -q TauD2.fasta -s JMGX01000001.1.cluster003.gbk --g Picking mode gbk/RAST /opt/corason/CORASON/gbkIndex.pl CORASON_GENOMES /opt/corason/CORASONDirectory CORASON_GENOMES rmdir: failed to remove '/home/output/GENOMES': No such file or directory cleaning old files.... /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES BGC0000715.1.cluster001.gbk 100001 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JMGX01000001.1.cluster003.gbk 100002 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JMGX01000001.1.cluster009.gbk 100003 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JMQG01000002.1.cluster016.gbk 100004 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOBV01000001.1.cluster003.gbk 100005 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOBV01000001.1.cluster044.gbk 100006 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOBW01000001.1.cluster001.gbk 100007 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOBW01000001.1.cluster018.gbk 100008 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOBW01000001.1.cluster027.gbk 100009 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOES01000001.1.cluster004.gbk 100010 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOES01000001.1.cluster049.gbk 100011 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOHJ01000001.1.cluster020.gbk 100012 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOIW01000001.1.cluster027.gbk 100013 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOIW01000001.1.cluster028.gbk 100014 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOJM01000001.1.cluster017.gbk 100015 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOJM01000001.1.cluster022.gbk 100016 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JOJM01000001.1.cluster024.gbk 100017 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES JPRA01000006.1.cluster028.gbk 100018 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES KL589150.1.cluster015.gbk 100019 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES LGCX01000001.1.cluster014.gbk 100020 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES LMFT01000001.1.cluster017.gbk 100021 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES MDDK01000001.1.cluster053.gbk 100022 /opt/corason/CORASON /opt/corason/CORASON/gbk_to_fasta.pl CORASON_GENOMES NC1.1.cluster031.gbk 100023 /opt/corason/CORASON rast=Corason_Rast.IDs special=100002

########################################################## Welcome to CORASON

-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. . |||||\ /||||||\ /||||||\ /||||||\ /||||||\ /||||||\ /| |/ ||||||/ ||||||/ ||||||/ ||||||/ ||||||/ ||||| ~ -~-`-~-`-~-~ -~-`-~-`-~-

         .-"    "-.     .-"     "-.
         /          `. .'            \
        |             "               \
        |             Y               |

___ | __/__ ____ / _ _/ `/ / _ \ / / / // / / / // /( )/ // / / / / __/ __/// _,/ // \/// // \ /' \ /' \ /' \ /' \ /' \ /' \ /' Y

CORASON-BGC

CORe Analysis of Syntenic Orthologs Natural Product-Biosynthetic Gene Cluster

########################################################## Your current directory is /home/output, local path output

You will use antiSMASH file none I must check TauD2.fasta is a fasta file Your cluster is located on organism number 100002 Default e-value=1E-15 Your bitscore is set to 0, you can use a positive bitscore to reduce your hunchs the radio of your cluster is 10 Minimal e-value to be consider an homologous of a cluster member is: 1E-3 Minimal e-value for ortho groups in core 1E-3 You are rescaling gene size by a factor: 85000 Your rast ids file is Corason_Rast.IDs All genomes would be procesed You will explore 23 genomes /opt/corason/CORASON/CoreCluster.pl -q TauD2.fasta -s 100002 -e_value 1E-15 -b 0 -cluster_radio 10 -e_core 1E-3 -e_cluster 1E-3 -rescale 85000 -l 100001,100002,100003,100004,100005,100006,100007,100008,100009,100010,100011,100012,100013,100014,100015,100016,100017,100018,100019,100020,100021,100022,100023 -num 23 -rast_ids Corason_Rast.IDs -antismash none Searching sequences from query (/opt/corason/CORASON/1_Context_text.pl) /opt/corason/CORASON/1_Context_text.pl -q TauD2.fasta -s 100002 -e_value 1E-15 -b 0 -cluster_radio 10 -e_cluster 1E-3 -r 85000 -l 100001,100002,100003,100004,100005,100006,100007,100008,100009,100010,100011,100012,100013,100014,100015,100016,100017,100018,100019,100020,100021,100022,100023 -n 23 -rast_ids Corason_Rast.IDs -type prots -makedb -antismash none -dir_scripts /opt/corason/CORASON

dir_scripts /opt/corason/CORASON mkdir: cannot create directory '/home/output/TauD2.fasta-output': File exists I will search homologous genes in organisms I will create a Database with selected genomes prots type

Aminoacid data will be analized /opt/corason/CORASON/header.pl GENOMES Corason_Rast.IDs /home/output/TauD2.fasta-output pause before makeDB makeblastdb -in /home/output/TauD2.fasta-output/TempConcatenados.faa -dbtype prot -out /home/output/TauD2.fasta-output/temDatabase.dbProtein db was created Looking for hits homologous gene search finished Searching for homologous gene in clusters 13 gen were found surrounding query, cluster radio can not exceed this radio. I have colored genes according to homology Now I will produce the *.input file Use of uninitialized value $hit in string eq at /opt/corason/CORASON/1_Context_text.pl line 272. Use of uninitialized value $hit in string eq at /opt/corason/CORASON/1_Context_text.pl line 272. Use of uninitialized value $hit in string eq at /opt/corason/CORASON/1_Context_text.pl line 272. Use of uninitialized value $hit in string eq at /opt/corason/CORASON/1_Context_text.pl line 272. Use of uninitialized value $hit in string eq at /opt/corason/CORASON/1_Context_text.pl line 272. Use of uninitialized value $hit in string eq at /opt/corason/CORASON/1_Context_text.pl line 272. Use of uninitialized value $hit in string eq at /opt/corason/CORASON/1_Context_text.pl line 272. Use of uninitialized value $hit in string eq at /opt/corason/CORASON/1_Context_text.pl line 272. Use of uninitialized value $hit in string eq at /opt/corason/CORASON/1_Context_text.pl line 272. Use of uninitialized value $hit in string eq at /opt/corason/CORASON/1_Context_text.pl line 272. Sequences search finished

Analizing cluster with hits according to the query sequence

Can't exec "1": No such file or directory at /opt/corason/CORASON/ReadingInputs.pl line 17.

--------------------- WARNING --------------------- MSG: Can not set Bio::Location::Simple::end() equal to start; start not set

--------------------- WARNING --------------------- MSG: Can not set Bio::Location::Simple::end() equal to start; start not set

--------------------- WARNING --------------------- MSG: Can not set Bio::Location::Simple::end() equal to start; start not set

--------------------- WARNING --------------------- MSG: Can not set Bio::Location::Simple::end() equal to start; start not set

--------------------- WARNING --------------------- MSG: Can not set Bio::Location::Simple::end() equal to start; start not set

--------------------- WARNING --------------------- MSG: Can not set Bio::Location::Simple::end() equal to start; start not set

--------------------- WARNING --------------------- MSG: Can not set Bio::Location::Simple::end() equal to start; start not set

--------------------- WARNING --------------------- MSG: Can not set Bio::Location::Simple::end() equal to start; start not set

There are 5 similar clusters Creating query hits tree, without considering the core-clusters

Aligning Sequences

Shaving alignments with Gblocks

File not in NBRF/PIR format or too few sequences in the alignment: 0

Execution terminated Couldn't open /home/output/TauD2.fasta-output/PrincipalHits.muscle-gb file No such file or directory at /opt/corason/CORASON/RenamePrincipalHits.pl line 11. FastTree Version 2.1.11 SSE3 Alignment: /home/output/TauD2.fasta-output/RightNamesPrincipalHits.txt Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000 Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1 TopHits: 1.00*sqrtN close=default refresh=0.80 ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories Cannot read /home/output/TauD2.fasta-output/RightNamesPrincipalHits.txt Searching genetic core on selected clusters /opt/corason/CORASON/2_OrthoGroups.pl -e_core 1E-3 -list 100001_1,100002_29,100005_7,100007_64,100010_7 -num 5 -rast_ids Corason_Rast.IDs -outname /home/output/TauD2.fasta-output -dir_scripts /opt/corason/CORASON I will run allvsall with blast /home/output/TauD2.fasta-output/Coreoutput.blast You want ortho groups of the following genomes 100001_1 100002_29 100005_7 100007_64 100010_7 Now finding Best Bidirectional Hits List Selecting List that contains orthologs from all desired genomes Starting Star groups num 5 list 100001_1,100002_29,100005_7,100007_64,100010_7 Starting stars /opt/corason/CORASON/SearchAminoacidsFromCore.pl 100001_1,100002_29,100005_7,100007_64,100010_7 /home/output/TauD2.fasta-output Done! /opt/corason/CORASON/ReadReaction 100001_1,100002_29,100005_7,100007_64,100010_7 5 /home/output/TauD2.fasta-output rm: cannot remove '/home/output/TauD2.fasta-output/CORASON/FUNCTION': No such file or directory Core finished!

There is a core with at least two genes on this cluster Best cluster /home/output/TauD2.fasta-output/100002_29 Best cluster /home/output/TauD2.fasta-output cut -f1,2 /home/output/TauD2.fasta-output/CORASON/FUNCTION/100002_29.core.function

Aligning...

/home/output/TauD2.fasta-output/CORASON

&align 1,5,/home/output/TauD2.fasta-output/CORASON,100001_1 100002_29 100005_7 100007_64 100010_7 Couldnt open /home/output/TauD2.fasta-output/CORASON/ALIGNMENTS_GB/1.muscle.pir No such file or directory Sequences were aligned

Creating aminoacid core cluster matrix.. directory /home/output/TauD2.fasta-output/CORASON/ALIGNMENTS_GB will be open Se abrio el directorio /home/output/TauD2.fasta-output/CORASON/ALIGNMENTS_GB con los archivos numericos

Can't open /home/output/TauD2.fasta-output/CORASON/CONCATENADOS/: No such file or directory. couldn't open /home/output/TauD2.fasta-output/CORASON/CONCATENADOS/1 No such file or directory at /opt/corason/CORASON/Concatenador.pl line 86. /opt/corason/CORASON/Rename_Ids_Star_Tree.pl Corason_Rast.IDs /home/output/TauD2.fasta-output rm: cannot remove '/home/output/TauD2.fasta-output/RightNames.txt': No such file or directory Couldn't open /home/output/TauD2.fasta-output/SalidaConcatenada.txt file No such file or directory at /opt/corason/CORASON/Rename_Ids_Star_Tree.pl line 11. Can't open /home/output/TauD2.fasta-output/RightNames.txt: No such file or directory. Formating matrix.. FastTree Version 2.1.11 SSE3 Alignment: /home/output/TauD2.fasta-output/RightNames.txt Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000 Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1 TopHits: 1.00sqrtN close=default refresh=0.80 ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories Cannot read /home/output/TauD2.fasta-output/RightNames.txt nw_topology -b -IL /home/output/TauD2.fasta-output/TauD2.fasta_BGC.tre | nw_display -b 'opacity:0' -v 40 -s - >/home/output/TauD2.fasta-output/TauD2.fasta_tree.svgI will draw SVG clusters with concatenated tree order /home/output/TauD2.fasta-output outname

Sequences didnt align, I will draw SVG clusters with the single hits blast order grep: /home/output/TauD2.fasta-output//home/output/TauD2.fasta-output.BLAST: No such file or directory grep: /home/output/TauD2.fasta-output//home/output/TauD2.fasta-output.BLAST: No such file or directory grep: /home/output/TauD2.fasta-output//home/output/TauD2.fasta-output.BLAST: No such file or directory grep: /home/output/TauD2.fasta-output//home/output/TauD2.fasta-output.BLAST: No such file or directory grep: /home/output/TauD2.fasta-output//home/output/TauD2.fasta-output.BLAST: No such file or directory

Draw Now SVG file will be generated with inputs:

/opt/corason/CORASON/3_Draw.pl 85000 /home/output/TauD2.fasta-output TauD2.fastaUse of uninitialized value $INPUTS in scalar chop at /opt/corason/CORASON/CoreCluster.pl line 281. Use of uninitialized value $INPUTS in concatenation (.) or string at /opt/corason/CORASON/CoreCluster.pl line 230. Use of uninitialized value $INPUTS in concatenation (.) or string at /opt/corason/CORASON/CoreCluster.pl line 231. Use of uninitialized value $INPUTS in concatenation (.) or string at /opt/corason/CORASON/CoreCluster.pl line 232. couldn open frequency file TauD2.fasta/Frequency Not a directory at /opt/corason/CORASON/3_Draw.pl line 113. SVG file generated

mv: cannot stat '/home/output/TauD2.fasta-output/Contextos.svg': No such file or directory Cleaning temporary files rm: cannot remove '/home/output/TauD2.fasta-output/PrincipalHits.muscle-gb.htm': No such file or directory rm: cannot remove '/home/output/TauD2.fasta-output/*.txt': No such file or directory rm: cannot remove '/home/output/TauD2.fasta-output/CORASON_GENOMES': No such file or directory mv TauD2.fasta /home/output/Done Have a nice day

nselem commented 1 month ago

Hello, sorry for the long delay. You can write an email nselem@matmor.unam.mx, we can set a zoom call and try to solve it.