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FEI38750 / MTD

MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
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The installations is stuck when building a new human database #4

Open leonorrib opened 1 year ago

leonorrib commented 1 year ago

Dear authors,

I've been trying to install the MTD software for a few times but I'm always encountering the same issue which is that when creating the new human db the installations just stays trying to do so but it doesn't move on. The expected file with the human database is emtpy all the time. Do you have any idea on how to fix it or how I could figure out what's the problem behind this?

Here I share with you the latest messages provided by the installation:

Building a new DB, current time: 02/18/2023 17:22:40
New DB name:   /path/MTD/human_blastdb/human_blastdb
New DB title:  /path/MTD/hisat2_index_human/genome.fa
Sequence type: Nucleotide
Deleted existing Nucleotide BLAST database named /path/MTD/human_blastdb/human_blastdb
Keep MBits: T
Maximum file size: 1000000000B

Best regards, Leonor

leonorrib commented 1 year ago

Hello :) @FEI38750

Could you look into the issue I opened two weeks ago? I'm still having that issue :)

Have a nice day, Leonor

FEI38750 commented 1 year ago

Could you please try if "makeblastdb" functional by typing

conda activate MTD makeblastdb

leonorrib commented 1 year ago

Thank you for the suggestion. Should I try it in parallel to the installation? The installation is still running, just stuck at that point I mentioned above.

FEI38750 commented 1 year ago

Yes, you can check it in parallel. How long does the installation stuck at that step?

leonorrib commented 1 year ago

Ok, I'll try. It's been stuck for three weeks now :)

FEI38750 commented 1 year ago

Maybe something is wrong with the "makeblastdb". We can bypass this step if you would not use the Magic-BLAST for alignment. Still can use Hisat2 which is the default method for reads alignment. Just search "# Create a BLAST database for Magic-BLAST" on the MTD/Install.sh script and make the lines of makeblastdb as comments.

leonorrib commented 1 year ago

I just checked the commands you suggested above and I would say that makeblastdb works fine, as far as I can see. This is the output of the commands:

(MTD) $ makeblastdb
USAGE
  makeblastdb [-h] [-help] [-in input_file] [-input_type type]
    -dbtype molecule_type [-title database_title] [-parse_seqids]
    [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
    [-mask_desc mask_algo_descriptions] [-gi_mask]
    [-gi_mask_name gi_based_mask_names] [-out database_name]
    [-blastdb_version version] [-max_file_sz number_of_bytes]
    [-logfile File_Name] [-taxid TaxID] [-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
   Application to create BLAST databases, version 2.10.1+

Use '-help' to print detailed descriptions of command line arguments
========================================================================

Error: Argument "dbtype". Mandatory value is missing:  `String, `nucl', `prot''
Error:  (CArgException::eNoArg) Argument "dbtype". Mandatory value is missing:  `String, `nucl', `prot''

I'll do what you suggest to skip that step. I'll post here the outcome of it.

leonorrib commented 1 year ago

Dear Fei,

The installation completed fine. I'll test it and get back to you afterwards.

Best regards, Leonor

leonorrib commented 1 year ago

Dear @FEI38750 ,

I completed running MTD on my data. There are some error messages. Perhaps the main one is this one: ERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the database version v30 . Please update your version of MetaPhlAn2 to v3.0.

Do you know how it can be solved?

Best regards, Leonor