[2023-06-08 18:46:12,027] [INFO] DFAST_QC pipeline started.
[2023-06-08 18:46:12,030] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 18:46:12,030] [INFO] DQC Reference Directory: /var/lib/cwl/stg01c2e0f4-76cd-4517-a998-45bb069e005b/dqc_reference
[2023-06-08 18:46:14,313] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 18:46:14,313] [INFO] Task started: Prodigal
[2023-06-08 18:46:14,314] [INFO] Running command: gunzip -c /var/lib/cwl/stgb697247c-d626-4cef-9126-8a407f7727cf/GCA_945877705.1_MoE-02may19-71_genomic.fna.gz | prodigal -d GCA_945877705.1_MoE-02may19-71_genomic.fna/cds.fna -a GCA_945877705.1_MoE-02may19-71_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 18:46:31,274] [INFO] Task succeeded: Prodigal
[2023-06-08 18:46:31,275] [INFO] Task started: HMMsearch
[2023-06-08 18:46:31,275] [INFO] Running command: hmmsearch --tblout GCA_945877705.1_MoE-02may19-71_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01c2e0f4-76cd-4517-a998-45bb069e005b/dqc_reference/reference_markers.hmm GCA_945877705.1_MoE-02may19-71_genomic.fna/protein.faa > /dev/null
[2023-06-08 18:46:31,510] [INFO] Task succeeded: HMMsearch
[2023-06-08 18:46:31,512] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb697247c-d626-4cef-9126-8a407f7727cf/GCA_945877705.1_MoE-02may19-71_genomic.fna.gz]
[2023-06-08 18:46:31,540] [INFO] Query marker FASTA was written to GCA_945877705.1_MoE-02may19-71_genomic.fna/markers.fasta
[2023-06-08 18:46:31,541] [INFO] Task started: Blastn
[2023-06-08 18:46:31,541] [INFO] Running command: blastn -query GCA_945877705.1_MoE-02may19-71_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c2e0f4-76cd-4517-a998-45bb069e005b/dqc_reference/reference_markers.fasta -out GCA_945877705.1_MoE-02may19-71_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:46:32,211] [INFO] Task succeeded: Blastn
[2023-06-08 18:46:32,216] [INFO] Selected 23 target genomes.
[2023-06-08 18:46:32,217] [INFO] Target genome list was writen to GCA_945877705.1_MoE-02may19-71_genomic.fna/target_genomes.txt
[2023-06-08 18:46:32,221] [INFO] Task started: fastANI
[2023-06-08 18:46:32,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgb697247c-d626-4cef-9126-8a407f7727cf/GCA_945877705.1_MoE-02may19-71_genomic.fna.gz --refList GCA_945877705.1_MoE-02may19-71_genomic.fna/target_genomes.txt --output GCA_945877705.1_MoE-02may19-71_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 18:46:49,453] [INFO] Task succeeded: fastANI
[2023-06-08 18:46:49,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01c2e0f4-76cd-4517-a998-45bb069e005b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 18:46:49,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01c2e0f4-76cd-4517-a998-45bb069e005b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 18:46:49,465] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 18:46:49,466] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 18:46:49,466] [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
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	75.8591	81	762	95	below_threshold
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	75.85	53	762	95	below_threshold
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	75.8284	82	762	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	74.664	53	762	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	74.6378	61	762	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 18:46:49,468] [INFO] DFAST Taxonomy check result was written to GCA_945877705.1_MoE-02may19-71_genomic.fna/tc_result.tsv
[2023-06-08 18:46:49,468] [INFO] ===== Taxonomy check completed =====
[2023-06-08 18:46:49,469] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 18:46:49,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01c2e0f4-76cd-4517-a998-45bb069e005b/dqc_reference/checkm_data
[2023-06-08 18:46:49,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 18:46:49,503] [INFO] Task started: CheckM
[2023-06-08 18:46:49,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945877705.1_MoE-02may19-71_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945877705.1_MoE-02may19-71_genomic.fna/checkm_input GCA_945877705.1_MoE-02may19-71_genomic.fna/checkm_result
[2023-06-08 18:47:37,547] [INFO] Task succeeded: CheckM
[2023-06-08 18:47:37,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 18:47:37,576] [INFO] ===== Completeness check finished =====
[2023-06-08 18:47:37,576] [INFO] ===== Start GTDB Search =====
[2023-06-08 18:47:37,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945877705.1_MoE-02may19-71_genomic.fna/markers.fasta)
[2023-06-08 18:47:37,577] [INFO] Task started: Blastn
[2023-06-08 18:47:37,577] [INFO] Running command: blastn -query GCA_945877705.1_MoE-02may19-71_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c2e0f4-76cd-4517-a998-45bb069e005b/dqc_reference/reference_markers_gtdb.fasta -out GCA_945877705.1_MoE-02may19-71_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:47:38,754] [INFO] Task succeeded: Blastn
[2023-06-08 18:47:38,759] [INFO] Selected 9 target genomes.
[2023-06-08 18:47:38,759] [INFO] Target genome list was writen to GCA_945877705.1_MoE-02may19-71_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 18:47:38,772] [INFO] Task started: fastANI
[2023-06-08 18:47:38,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgb697247c-d626-4cef-9126-8a407f7727cf/GCA_945877705.1_MoE-02may19-71_genomic.fna.gz --refList GCA_945877705.1_MoE-02may19-71_genomic.fna/target_genomes_gtdb.txt --output GCA_945877705.1_MoE-02may19-71_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 18:47:46,686] [INFO] Task succeeded: fastANI
[2023-06-08 18:47:46,700] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 18:47:46,701] [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_009695395.1	s__SXTU01 sp009695395	95.1611	476	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005791875.1	s__SXTU01 sp005791875	86.046	600	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.67	99.31	0.92	0.90	5	-
GCA_016235545.1	s__SXTU01 sp016235545	85.6904	606	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773355.1	s__SXTU01 sp009773355	85.532	644	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.99	99.99	0.98	0.97	3	-
GCA_903863315.1	s__SXTU01 sp903863315	82.4467	502	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009922615.1	s__SXTU01 sp009922615	82.2293	575	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.88	99.88	0.94	0.94	2	-
GCA_016871445.1	s__SXTU01 sp016871445	79.8202	439	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	98.73	98.73	0.87	0.87	2	-
GCA_016199935.1	s__JACQFS01 sp016199935	78.2823	319	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACQFS01;g__JACQFS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916195.1	s__CAIVQB01 sp903916195	77.1769	179	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	99.38	98.88	0.92	0.89	6	-
--------------------------------------------------------------------------------
[2023-06-08 18:47:46,703] [INFO] GTDB search result was written to GCA_945877705.1_MoE-02may19-71_genomic.fna/result_gtdb.tsv
[2023-06-08 18:47:46,703] [INFO] ===== GTDB Search completed =====
[2023-06-08 18:47:46,706] [INFO] DFAST_QC result json was written to GCA_945877705.1_MoE-02may19-71_genomic.fna/dqc_result.json
[2023-06-08 18:47:46,707] [INFO] DFAST_QC completed!
[2023-06-08 18:47:46,707] [INFO] Total running time: 0h1m35s