[2023-06-30 21:10:01,455] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:10:01,457] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:10:01,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ddc4d78-a0d5-4cce-a525-1957fae346d3/dqc_reference
[2023-06-30 21:10:03,577] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:10:03,578] [INFO] Task started: Prodigal
[2023-06-30 21:10:03,579] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dd028b0-d200-4b7f-aed7-00158bf26bef/GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna.gz | prodigal -d GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/cds.fna -a GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:10:09,783] [INFO] Task succeeded: Prodigal
[2023-06-30 21:10:09,784] [INFO] Task started: HMMsearch
[2023-06-30 21:10:09,784] [INFO] Running command: hmmsearch --tblout GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ddc4d78-a0d5-4cce-a525-1957fae346d3/dqc_reference/reference_markers.hmm GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:10:10,017] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:10:10,018] [INFO] Found 6/6 markers.
[2023-06-30 21:10:10,041] [INFO] Query marker FASTA was written to GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/markers.fasta
[2023-06-30 21:10:10,041] [INFO] Task started: Blastn
[2023-06-30 21:10:10,041] [INFO] Running command: blastn -query GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ddc4d78-a0d5-4cce-a525-1957fae346d3/dqc_reference/reference_markers.fasta -out GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:10:10,666] [INFO] Task succeeded: Blastn
[2023-06-30 21:10:10,670] [INFO] Selected 23 target genomes.
[2023-06-30 21:10:10,670] [INFO] Target genome list was writen to GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/target_genomes.txt
[2023-06-30 21:10:10,675] [INFO] Task started: fastANI
[2023-06-30 21:10:10,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dd028b0-d200-4b7f-aed7-00158bf26bef/GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna.gz --refList GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/target_genomes.txt --output GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:10:21,710] [INFO] Task succeeded: fastANI
[2023-06-30 21:10:21,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ddc4d78-a0d5-4cce-a525-1957fae346d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:10:21,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ddc4d78-a0d5-4cce-a525-1957fae346d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:10:21,714] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:10:21,714] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 21:10:21,715] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-30 21:10:21,717] [INFO] DFAST Taxonomy check result was written to GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/tc_result.tsv
[2023-06-30 21:10:21,718] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:10:21,718] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:10:21,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ddc4d78-a0d5-4cce-a525-1957fae346d3/dqc_reference/checkm_data
[2023-06-30 21:10:21,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:10:21,757] [INFO] Task started: CheckM
[2023-06-30 21:10:21,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/checkm_input GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/checkm_result
[2023-06-30 21:10:46,297] [INFO] Task succeeded: CheckM
[2023-06-30 21:10:46,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:10:46,320] [INFO] ===== Completeness check finished =====
[2023-06-30 21:10:46,320] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:10:46,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/markers.fasta)
[2023-06-30 21:10:46,321] [INFO] Task started: Blastn
[2023-06-30 21:10:46,321] [INFO] Running command: blastn -query GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ddc4d78-a0d5-4cce-a525-1957fae346d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:10:47,330] [INFO] Task succeeded: Blastn
[2023-06-30 21:10:47,335] [INFO] Selected 24 target genomes.
[2023-06-30 21:10:47,335] [INFO] Target genome list was writen to GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:10:47,352] [INFO] Task started: fastANI
[2023-06-30 21:10:47,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dd028b0-d200-4b7f-aed7-00158bf26bef/GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna.gz --refList GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:10:59,253] [INFO] Task succeeded: fastANI
[2023-06-30 21:10:59,260] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:10:59,260] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_905480645.1	s__Tateyamaria sp003445215	99.6488	750	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	98.75	98.35	0.86	0.66	9	conclusive
GCA_018668195.1	s__Tateyamaria sp018668195	76.8341	51	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 21:10:59,262] [INFO] GTDB search result was written to GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/result_gtdb.tsv
[2023-06-30 21:10:59,263] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:10:59,265] [INFO] DFAST_QC result json was written to GCA_943841345.1_20200310_METABAT_170_1-contigs.fa_genomic.fna/dqc_result.json
[2023-06-30 21:10:59,265] [INFO] DFAST_QC completed!
[2023-06-30 21:10:59,265] [INFO] Total running time: 0h0m58s