Why is this makeblastdb command not working? Ask Question 7 $egingroup$ I am trying to make local databases for the ncbi-blast+ package (version 2.60). I am doing so for 4 T-cell receptor genes. 3 of the 4 (TRAV, TRAJ, TRBV) have worked fine, but I am having problems with TRBJ. I say this makeblastdb has a -max_file_sz, set by default to 1GB. Can we increase this limit by default to 10GB or should we offer this as a parameter? makeblastdb -max_file_sz #63. Open bgruening opened this Issue Jun 9, 2015 · 15 comments Open My IDs not good enough for NCBI BLAST+ The blastdbcmd tool in the BLAST+ suite (replacing fastacmd in the C 'legacy' BLAST suite) lets you do a lot of clever things with a BLAST database. As long as you follow the baroque NCBI FASTA naming scheme you can do this with local BLAST databases too. A sufficiently close match between subsequences (denoted by arrows in the figure above, though matches are usually longer than illustrated here) is called a high-scoring pair (HSP), while a query sequence is said to hit a target sequence if they share one or more HSPs. Sometimes, however, the term "hit" is used loosely, without differentiating between the two. The Geneious User Manual has more detailed information on how to set this up. Note, if you wish to create pre-formatted BLAST databases from fasta files outside of Geneious, you can also run the BLAST+ executables from the command line using the makeblastdb command. SPAdes 3.5.0 Manual 1. About SPAdes 1.1. Supported data types 1.2. SPAdes pipeline 1.3. SPAdes performance 2. Installation 2.1. Downloading SPAdes Linux binaries 2.2. Downloading SPAdes binaries for Mac 2.3. Downloading and compiling SPAdes source code 2.4. Verifying your installation 3. Running SPAdes 3.1. SPAdes input 3.2. SPAdes command line John Chilton on makeblastdb fails with large files in a workflow. @peterjc @bgruening Given the mixed results of the fix - works for Peter cluster and my Docker testing but not Bjoern's