[2023-06-13 02:32:00,711] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:32:00,713] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:32:00,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6efe384-ca52-4c68-8199-b2d5e8a19ff0/dqc_reference
[2023-06-13 02:32:02,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:32:02,898] [INFO] Task started: Prodigal
[2023-06-13 02:32:02,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg40145f2a-b801-4e8d-b9b4-a116ee61ee26/GCA_022565695.1_ASM2256569v1_genomic.fna.gz | prodigal -d GCA_022565695.1_ASM2256569v1_genomic.fna/cds.fna -a GCA_022565695.1_ASM2256569v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:32:14,439] [INFO] Task succeeded: Prodigal
[2023-06-13 02:32:14,440] [INFO] Task started: HMMsearch
[2023-06-13 02:32:14,440] [INFO] Running command: hmmsearch --tblout GCA_022565695.1_ASM2256569v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6efe384-ca52-4c68-8199-b2d5e8a19ff0/dqc_reference/reference_markers.hmm GCA_022565695.1_ASM2256569v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:32:14,697] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:32:14,699] [INFO] Found 6/6 markers.
[2023-06-13 02:32:14,733] [INFO] Query marker FASTA was written to GCA_022565695.1_ASM2256569v1_genomic.fna/markers.fasta
[2023-06-13 02:32:14,733] [INFO] Task started: Blastn
[2023-06-13 02:32:14,733] [INFO] Running command: blastn -query GCA_022565695.1_ASM2256569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6efe384-ca52-4c68-8199-b2d5e8a19ff0/dqc_reference/reference_markers.fasta -out GCA_022565695.1_ASM2256569v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:32:15,518] [INFO] Task succeeded: Blastn
[2023-06-13 02:32:15,523] [INFO] Selected 15 target genomes.
[2023-06-13 02:32:15,523] [INFO] Target genome list was writen to GCA_022565695.1_ASM2256569v1_genomic.fna/target_genomes.txt
[2023-06-13 02:32:15,544] [INFO] Task started: fastANI
[2023-06-13 02:32:15,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg40145f2a-b801-4e8d-b9b4-a116ee61ee26/GCA_022565695.1_ASM2256569v1_genomic.fna.gz --refList GCA_022565695.1_ASM2256569v1_genomic.fna/target_genomes.txt --output GCA_022565695.1_ASM2256569v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:32:25,662] [INFO] Task succeeded: fastANI
[2023-06-13 02:32:25,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6efe384-ca52-4c68-8199-b2d5e8a19ff0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:32:25,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6efe384-ca52-4c68-8199-b2d5e8a19ff0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:32:25,676] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:32:25,676] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 02:32:25,676] [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
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	85.3733	940	1169	95	below_threshold
Alcanivorax indicus	strain=SW127	GCA_003259185.1	2202653	2202653	type	True	80.647	711	1169	95	below_threshold
Alcanivorax pacificus	strain=W11-5	GCA_000299335.2	1306787	1306787	type	True	79.1701	491	1169	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	78.37	298	1169	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	78.2132	288	1169	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	78.1209	313	1169	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	78.0408	321	1169	95	below_threshold
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	77.9435	281	1169	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	77.9346	312	1169	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	77.8303	246	1169	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	77.8156	259	1169	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	77.7397	221	1169	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.4253	114	1169	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	76.2951	122	1169	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	75.7048	70	1169	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:32:25,678] [INFO] DFAST Taxonomy check result was written to GCA_022565695.1_ASM2256569v1_genomic.fna/tc_result.tsv
[2023-06-13 02:32:25,679] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:32:25,679] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:32:25,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6efe384-ca52-4c68-8199-b2d5e8a19ff0/dqc_reference/checkm_data
[2023-06-13 02:32:25,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:32:25,719] [INFO] Task started: CheckM
[2023-06-13 02:32:25,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022565695.1_ASM2256569v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022565695.1_ASM2256569v1_genomic.fna/checkm_input GCA_022565695.1_ASM2256569v1_genomic.fna/checkm_result
[2023-06-13 02:33:03,217] [INFO] Task succeeded: CheckM
[2023-06-13 02:33:03,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:33:03,292] [INFO] ===== Completeness check finished =====
[2023-06-13 02:33:03,294] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:33:03,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022565695.1_ASM2256569v1_genomic.fna/markers.fasta)
[2023-06-13 02:33:03,295] [INFO] Task started: Blastn
[2023-06-13 02:33:03,295] [INFO] Running command: blastn -query GCA_022565695.1_ASM2256569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6efe384-ca52-4c68-8199-b2d5e8a19ff0/dqc_reference/reference_markers_gtdb.fasta -out GCA_022565695.1_ASM2256569v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:33:04,430] [INFO] Task succeeded: Blastn
[2023-06-13 02:33:04,434] [INFO] Selected 13 target genomes.
[2023-06-13 02:33:04,434] [INFO] Target genome list was writen to GCA_022565695.1_ASM2256569v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:33:04,441] [INFO] Task started: fastANI
[2023-06-13 02:33:04,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg40145f2a-b801-4e8d-b9b4-a116ee61ee26/GCA_022565695.1_ASM2256569v1_genomic.fna.gz --refList GCA_022565695.1_ASM2256569v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022565695.1_ASM2256569v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:33:13,608] [INFO] Task succeeded: fastANI
[2023-06-13 02:33:13,631] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 02:33:13,631] [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
GCF_003259185.1	s__Alcanivorax_A indicus	80.6558	710	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823245.1	s__Alcanivorax_A sp013823245	80.3631	623	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299335.2	s__Alcanivorax_A pacificus	79.1795	490	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846755.1	s__Alcanivorax_A sp009846755	79.0786	457	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794945.1	s__Alcanivorax sp009711585	78.1407	262	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCF_016906305.1	s__Alcanivorax marinus_B	78.1356	305	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794965.1	s__Alcanivorax sp017794965	78.078	264	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107995.1	s__Alcanivorax sp900107995	78.0366	278	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCA_003862375.1	s__Alcanivorax jadensis_A	77.9979	284	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.67	99.67	0.92	0.92	2	-
GCF_000756655.1	s__Alcanivorax jadensis	77.9428	281	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	77.9233	313	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCF_002864685.1	s__Alcanivorax mobilis	77.829	258	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.57	98.57	0.96	0.96	2	-
GCF_003597125.1	s__Alcanivorax profundi	77.7439	220	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.31	99.31	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-13 02:33:13,633] [INFO] GTDB search result was written to GCA_022565695.1_ASM2256569v1_genomic.fna/result_gtdb.tsv
[2023-06-13 02:33:13,634] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:33:13,641] [INFO] DFAST_QC result json was written to GCA_022565695.1_ASM2256569v1_genomic.fna/dqc_result.json
[2023-06-13 02:33:13,642] [INFO] DFAST_QC completed!
[2023-06-13 02:33:13,642] [INFO] Total running time: 0h1m13s