align

Create a multiple sequence alignment based on the AR53/BAC120 marker set.

Arguments

Files output

• [prefix].log

• [prefix].json

• [prefix].warnings.log

• align

  • [prefix].[domain].msa.fasta.gz

  • [prefix].[domain].user_msa.fasta.gz

  • [prefix].[domain].filtered.tsv

  • intermediate_results

    • [prefix].[domain].marker_info.tsv

Example

Input

gtdbtk align --identify_dir identify_output/ --out_dir align_output --cpus 3

Output

[2022-04-11 11:59:14] INFO: GTDB-Tk v2.0.0
[2022-04-11 11:59:14] INFO: gtdbtk align --identify_dir /tmp/gtdbtk/identify --out_dir /tmp/gtdbtk/align --cpus 2
[2022-04-11 11:59:14] INFO: Using GTDB-Tk reference data version r207: /srv/db/gtdbtk/official/release207
[2022-04-11 11:59:15] INFO: Aligning markers in 3 genomes with 2 CPUs.
[2022-04-11 11:59:16] INFO: Processing 3 genomes identified as archaeal.
[2022-04-11 11:59:16] INFO: Read concatenated alignment for 3,412 GTDB genomes.
[2022-04-11 11:59:16] TASK: Generating concatenated alignment for each marker.
[2022-04-11 11:59:16] INFO: Completed 3 genomes in 0.01 seconds (139.73 genomes/second).
[2022-04-11 11:59:16] TASK: Aligning 52 identified markers using hmmalign 3.1b2 (February 2015).
[2022-04-11 11:59:17] INFO: Completed 52 markers in 0.86 seconds (60.66 markers/second).
[2022-04-11 11:59:17] TASK: Masking columns of archaeal multiple sequence alignment using canonical mask.
[2022-04-11 11:59:21] INFO: Completed 3,414 sequences in 4.19 seconds (815.22 sequences/second).
[2022-04-11 11:59:21] INFO: Masked archaeal alignment from 13,540 to 10,153 AAs.
[2022-04-11 11:59:21] INFO: 0 archaeal user genomes have amino acids in <10.0% of columns in filtered MSA.
[2022-04-11 11:59:21] INFO: Creating concatenated alignment for 3,414 archaeal GTDB and user genomes.
[2022-04-11 11:59:23] INFO: Creating concatenated alignment for 3 archaeal user genomes.
[2022-04-11 11:59:23] INFO: Done.