Bioinformatics Recipe Cookbook

Run Parameters
Parameters used during the run:
No user parameters were set.
File List
Files created by the recipe run:
Output Messages
Messages printed to the standard output stream:
Connected to NCBI
The contents of 16SMicrobial.tar.gz are up to date in your system.

*** The first ten lines of accession number NR_026093
>NR_026093.1 Atopobium parvulum strain VPI 0546 16S ribosomal RNA gene, partial sequence
GCGAACGGCTGAGTAACACGTGGGCAACCTGCCCCTTTCATTGGGATAGCCACGGGAAACCGTGATAATACCGAATACTT
CGAGACTTCCGCATGGAAGACTCGAGAAAGCTCCGGCGGAGAGGGATGGCCCGCGGCCTGTTAGCTTGTTGGTGGGGTAA
CGGCCTACCAAGGCAATGATGGGTAGCTGGGTTGAGAGACCGACCAGCCAGATTGGGACTGAGACACGGCCCAGACTCCT
ACGGGAGGCAGCAGTGGGGAATCTTGCACAATGGGCGAAAGCCTGATGCAGCGACGCCGCGTGCGGGATGAAGGCCTTCG
GGTTGTAAACCGCTTTCAGCAGGGACGAGGCGAAAGTGACGGTACCTGCAGAAGAAGCCCCGGCTAACTACGTGCCAGCA
GCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTCATTGGGCGTAAAGCGCTCGTAGGCGGTCTGTTAGGTCGGGA
GTTAAATCCGGGGGCTCAACCCCCGCTCGCTCTCGATACCGGCAGACTTGAGTTTGGTAGGGGAAGGTGGAATTCCTAGT
GTAGCGGTGGAATGCGCAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCCTTCTGGGCCATAACTGACGCTGAGGAGC
GAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGATGGACACTAGGTGTGGGGGAGTATT

*** Limit to the first 20 bases:
>NR_026093.1 Atopobium parvulum strain VPI 0546 16S ribosomal RNA gene, partial sequence
GCGAACGGCTGAGTAACACG

*** Dump all sequences of the database into file all.fa

*** Format the output using a format string: accession number and sequence length
NR_118889.1 1300
NR_118899.1 1367
NR_074334.1 1492
NR_118873.1 1492
NR_119237.1 1492
NR_118890.1 1331
NR_044838.1 1454
NR_118908.1 1343
NR_118900.1 1376
NR_044822.1 1255

*** How many database sequences in the database
20748

*** Top 10 common gene sequence starts:
   1903 AGAGTTTGATCCTGGCTCAG
   1243 GACGAACGCTGGCGGCGTGC
    591 ATTGAACGCTGGCGGCAGGC
    415 GATGAACGCTAGCGGCAGGC
    339 ATTCCGGTTGATCCTGCCGG
    336 AACGAACGCTGGCGGCAGGC
    331 AGAGTTTGATCATGGCTCAG
    273 ATTGAACGCTGGCGGCATGC
    236 ACGAACGCTGGCGGCGTGCT
    215 TAGAGTTTGATCCTGGCTCA

*** Building the blast database


Building a new DB, current time: 10/08/2018 14:55:04
New DB name:   /export/sites/biostar-engine/export/media/jobs/job-15debb58/xdb/my16S
New DB title:  all.fa
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 20470 sequences in 0.674629 seconds.

*** Top 10 common gene sequence starts using the newly created database:
   1903 AGAGTTTGATCCTGGCTCAG
   1243 GACGAACGCTGGCGGCGTGC
    591 ATTGAACGCTGGCGGCAGGC
    415 GATGAACGCTAGCGGCAGGC
    339 ATTCCGGTTGATCCTGCCGG
    336 AACGAACGCTGGCGGCAGGC
    331 AGAGTTTGATCATGGCTCAG
    273 ATTGAACGCTGGCGGCATGC
    236 ACGAACGCTGGCGGCGTGCT
    215 TAGAGTTTGATCCTGGCTCA
Other Messages
Messages printed to the standard error stream:

    

Powered by the release 1.4