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Open palvinaveen opened this issue 9 months ago • 3 comments

Picking mode gbk/RAST special org: 1433767 rast=los7Rast.ids special=1433767

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

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CORASON-BGC

CORe Analysis of Syntenic Orthologs Natural Product-Biosynthetic Gene Cluster

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

You will use antiSMASH file none I must check A0A139GIE5.query is a fasta file Your cluster is located on organism number 1433767 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 los7Rast.ids All genomes would be procesed You will explore 6 genomes /opt/corason/CORASON/CoreCluster.pl -q A0A139GIE5.query -s 1433767 -e_value 1E-15 -b 0 -cluster_radio 10 -e_core 1E-3 -e_cluster 1E-3 -rescale 85000 -l 1433767 6666666.1170174 Tolypothrix sp. PCC 7601,1433766 6666666.1170173 Microcystis aeruginosa,1433765 6666666.1170172 Microcystis aeruginosa NIES-843 ,1433764 6666666.1170171 Anabaenopsis elenkinii CCIBt3563,1433763 6666666.1170170 Microcystis aeruginosa PCC 7806SL,1433762 6666666.1170169 Planktothrix agardhii ,1433761 6666666.1170168 Planktothrix agardhii NIVA-CYA 15 -num 6 -rast_ids los7Rast.ids -antismash none Searching sequences from query (/opt/corason/CORASON/1_Context_text.pl) /opt/corason/CORASON/1_Context_text.pl -q A0A139GIE5.query -s 1433767 -e_value 1E-15 -b 0 -cluster_radio 10 -e_cluster 1E-3 -r 85000 -l 1433767 -n 6 -rast_ids los7Rast.ids -type prots -makedb -antismash none -dir_scripts /opt/corason/CORASON

dir_scripts /opt/corason/CORASON mkdir: cannot create directory '/home/output/A0A139GIE5.query-output': File exists I will search homologous genes in organisms mkdir: cannot create directory '/home/output/A0A139GIE5.query-output/MINI': File exists I will create a Database with selected genomes prots type

Aminoacid data will be analized /opt/corason/CORASON/header.pl GENOMES los7Rast.ids /home/output/A0A139GIE5.query-output Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/header.pl line 29, <ALL> line 1. GENOMES/1433767 6666666.1170174 Tolypothrix sp. PCC 7601.faa does not exists No such file or directory at /opt/corason/CORASON/header.pl line 32, <ALL> line 1. pause before makeDB makeblastdb -in /home/output/A0A139GIE5.query-output/TempConcatenados.faa -dbtype prot -out /home/output/A0A139GIE5.query-output/temDatabase.dbProtein db was created Looking for hits homologous gene search finished Searching for homologous gene in clusters I have colored genes according to homology Now I will produce the *.input file Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 251. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. Use of uninitialized value in concatenation (.) or string at /opt/corason/CORASON/1_Context_text.pl line 300. 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. Couldnt open 1433767 No such file or directory at /opt/corason/CORASON/GbkCreator.pl line 76. There are 1 similar clusters Creating query hits tree, without considering the core-clusters

Aligning Sequences

Shaving alignments with Gblocks

  • File not opened *

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

Execution terminated Couldn't open /home/output/A0A139GIE5.query-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/A0A139GIE5.query-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/A0A139GIE5.query-output/RightNamesPrincipalHits.txt Searching genetic core on selected clusters /opt/corason/CORASON/2_OrthoGroups.pl -e_core 1E-3 -list 1433767_23 -num 1 -rast_ids los7Rast.ids -outname /home/output/A0A139GIE5.query-output -dir_scripts /opt/corason/CORASON I will run allvsall with blast /home/output/A0A139GIE5.query-output/Coremydir.blast You want ortho groups of the following genomes 1433767_23 Now finding Best Bidirectional Hits List Selecting List that contains orthologs from all desired genomes Starting Star groups num 1 list 1433767_23 Starting stars /opt/corason/CORASON/SearchAminoacidsFromCore.pl 1433767_23 /home/output/A0A139GIE5.query-output Done! /opt/corason/CORASON/ReadReaction 1433767_23 1 /home/output/A0A139GIE5.query-output rm: cannot remove '/home/output/A0A139GIE5.query-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/A0A139GIE5.query-output/1433767_23 Best cluster /home/output/A0A139GIE5.query-output cut -f1,2 /home/output/A0A139GIE5.query-output/CORASON/FUNCTION/1433767_23.core.function

Aligning...

/home/output/A0A139GIE5.query-output/CORASON

&align 1,1,/home/output/A0A139GIE5.query-output/CORASON,1433767_23 Couldnt open /home/output/A0A139GIE5.query-output/CORASON/ALIGNMENTS_GB/1.muscle.pir No such file or directory Sequences were aligned

Creating aminoacid core cluster matrix.. directory /home/output/A0A139GIE5.query-output/CORASON/ALIGNMENTS_GB will be open Se abrio el directorio /home/output/A0A139GIE5.query-output/CORASON/ALIGNMENTS_GB con los archivos numericos

Can't open /home/output/A0A139GIE5.query-output/CORASON/CONCATENADOS/: No such file or directory. couldn't open /home/output/A0A139GIE5.query-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 los7Rast.ids /home/output/A0A139GIE5.query-output rm: cannot remove '/home/output/A0A139GIE5.query-output/RightNames.txt': No such file or directory Couldn't open /home/output/A0A139GIE5.query-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/A0A139GIE5.query-output/RightNames.txt: No such file or directory. Formating matrix.. FastTree Version 2.1.11 SSE3 Alignment: /home/output/A0A139GIE5.query-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/A0A139GIE5.query-output/RightNames.txt nw_topology -b -IL /home/output/A0A139GIE5.query-output/A0A139GIE5.query_BGC.tre | nw_display -b 'opacity:0' -v 40 -s - >/home/output/A0A139GIE5.query-output/A0A139GIE5.query_tree.svgI will draw SVG clusters with concatenated tree order /home/output/A0A139GIE5.query-output outname

Sequences didnt align, I will draw SVG clusters with the single hits blast order grep: /home/output/A0A139GIE5.query-output//home/output/A0A139GIE5.query-output.BLAST: No such file or directory Use of uninitialized value $INPUTS in scalar chop at /opt/corason/CORASON/CoreCluster.pl line 281.

Draw Use of uninitialized value $INPUTS in concatenation (.) or string at /opt/corason/CORASON/CoreCluster.pl line 230. Now SVG file will be generated with inputs:

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. /opt/corason/CORASON/3_Draw.pl 85000 /home/output/A0A139GIE5.query-output A0A139GIE5.querycouldn open frequency file A0A139GIE5.query/Frequency Not a directory at /opt/corason/CORASON/3_Draw.pl line 113. SVG file generated

mv: cannot stat '/home/output/A0A139GIE5.query-output/Contextos.svg': No such file or directory Cleaning temporary files rm: cannot remove '/home/output/A0A139GIE5.query-output/PrincipalHits.muscle-gb.htm': No such file or directory rm: cannot remove '/home/output/A0A139GIE5.query-output/*.txt': No such file or directory rm: cannot remove '/home/output/A0A139GIE5.query-output/CORASON_GENOMES': No such file or directory mv A0A139GIE5.query /home/output/Done Have a nice day

I am unable to generate .svg file with the combination of Increase and Decrease number of data size@joyliu19,also edited the Draw.pl as you mentioned in the issue section even i tried the exmple file but it is unable to generate the .svg file. can you please help me to resolve this why i am getting this error ? Thank you.

your sincearly Naveen

palvinaveen avatar May 27 '24 11:05 palvinaveen