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bioinfo-ut / StrainSeeker

A bacterial identification program for fast identification of bacterial strains from raw sequencing reads
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database binary #7

Open Gagi1993 opened 1 year ago

Gagi1993 commented 1 year ago

Hello,

I'm sorry for bothering you , I have a question. I came a cross your site and i was wondering if i can try to use it on viruses. i created rooted nw tree with my own fasta files and run this command:

perl builder.pl -w 32 -d fasta -n temp.nwk -o covid_db

and database was created but only with info.txt no binary this is the log of the command

CONVERTING NEWICK... CREATING LISTS FOR LEAVES... Creating node lists: union of children and remove redundant... Generating nodes: 11 of 15 Generating nodes: 13 of 15 Generating nodes: 14 of 15 Generating nodes: 15 of 15 CREATING LARGE UNION FOR MULTIPLE OCCURANCE REMOVAL... Making union of lists, remaining: 14 Making union of lists, remaining: 7 Making union of lists, remaining: 3 Making union of lists, remaining: 1 ELIMINATING K-MERS OCCURING IN MULTIPLE NODES Eliminate multiple occurring: all remaining GET INITAL K-MER COUNT IN LISTS... REMOVING UNUSED LISTS... REDUCING LISTS... Use of uninitialized value $cmd in string ne at builder.pl line 654. Renaming all subset files and get new counts Writing tree data to info.txt CREATING BINARY FILE... Writing to temp text file StrainSeeker_temporary_text_fileSatApr151659102023.txt covid_db/2785EPI_ISL_16913337_32.list covid_db/N6_32.list covid_db/2807EPI_ISL_169133572023-02-01_32.list covid_db/N4_32.list covid_db/3179EPI_ISL_172477302023-02-23_32.list covid_db/N2_32.list covid_db/2993EPI_ISL_172682342023-02-06_32.list covid_db/3165EPI_ISL_172477232023-02-22_32.list covid_db/N1_32.list covid_db/2787EPI_ISL_16913339_32.list covid_db/2935EPI_ISL_172681772023-02-08_32.list covid_db/N5_32.list covid_db/2782EPI_ISL_16913334_32.list covid_db/N0_32.list covid_db/N3_32.list Converting into binary file... gmer_counter: trie.c:206: trie_node_branch_new: Assertion `nbits_this <= 52' failed.

Start and nwk convert: 0.0s Leaves generation: 2.0s Node generation and counts: 0.0s Large union generation for multiple occurance removal: 0.0s Multiple occurance removal: 0.0s Getting subroots: 0.0s Redundant removal: 0.0s List reducing: 0.0s Binary db creation: 1.0s Total run time: 3.0s

DONE Total 15 nodes of which 1 are subroots of which 0 are root-leaves. Warning messages produced: 0

I am wondering why gmer_counter failed and why ? I assume that this is the problem so if you maybe know how to fix? Or the problem is because i tried to create similar corona viruses ?

And one more question whenever i try to upload bacterial fastq on your web tool i get connection time error ?

Once again sorry for disturbing you

And thank you

gagi19993 commented 1 year ago

Hello,

i download the gmer_counter directly from genome tester and this error was fixed