[2024-01-25 18:01:50,687] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:01:50,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:01:50,689] [INFO] DQC Reference Directory: /var/lib/cwl/stgfef25dc0-1c36-485b-a3ba-aa097799277d/dqc_reference
[2024-01-25 18:01:51,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:01:51,788] [INFO] Task started: Prodigal
[2024-01-25 18:01:51,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg63e0d584-fa42-4170-9762-5057bb1239d5/GCF_003014535.1_ASM301453v1_genomic.fna.gz | prodigal -d GCF_003014535.1_ASM301453v1_genomic.fna/cds.fna -a GCF_003014535.1_ASM301453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:16,518] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:16,518] [INFO] Task started: HMMsearch
[2024-01-25 18:02:16,518] [INFO] Running command: hmmsearch --tblout GCF_003014535.1_ASM301453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfef25dc0-1c36-485b-a3ba-aa097799277d/dqc_reference/reference_markers.hmm GCF_003014535.1_ASM301453v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:16,790] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:16,791] [INFO] Found 6/6 markers.
[2024-01-25 18:02:16,838] [INFO] Query marker FASTA was written to GCF_003014535.1_ASM301453v1_genomic.fna/markers.fasta
[2024-01-25 18:02:16,839] [INFO] Task started: Blastn
[2024-01-25 18:02:16,839] [INFO] Running command: blastn -query GCF_003014535.1_ASM301453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfef25dc0-1c36-485b-a3ba-aa097799277d/dqc_reference/reference_markers.fasta -out GCF_003014535.1_ASM301453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:17,404] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:17,406] [INFO] Selected 18 target genomes.
[2024-01-25 18:02:17,407] [INFO] Target genome list was writen to GCF_003014535.1_ASM301453v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:17,417] [INFO] Task started: fastANI
[2024-01-25 18:02:17,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg63e0d584-fa42-4170-9762-5057bb1239d5/GCF_003014535.1_ASM301453v1_genomic.fna.gz --refList GCF_003014535.1_ASM301453v1_genomic.fna/target_genomes.txt --output GCF_003014535.1_ASM301453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:34,260] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:34,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfef25dc0-1c36-485b-a3ba-aa097799277d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:34,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfef25dc0-1c36-485b-a3ba-aa097799277d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:34,268] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:02:34,268] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:34,268] [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
Taibaiella chishuiensis	strain=CGMCC 1.12700	GCA_003014535.1	1434707	1434707	type	True	100.0	1930	1933	95	conclusive
Taibaiella helva	strain=F-4	GCA_003545695.1	2301235	2301235	type	True	77.6898	404	1933	95	below_threshold
Taibaiella koreensis	strain=THG-DT86	GCA_003545715.1	1268548	1268548	type	True	77.3926	382	1933	95	below_threshold
Taibaiella lutea	strain=KVB11	GCA_008629695.1	2608001	2608001	type	True	76.9405	147	1933	95	below_threshold
Edaphocola aurantiacus	strain=H2	GCA_019797745.1	2601682	2601682	type	True	76.8203	101	1933	95	below_threshold
Edaphocola flava	strain=HME-24	GCA_004118155.1	2499629	2499629	type	True	76.7018	103	1933	95	below_threshold
Flavipsychrobacter stenotrophus	strain=RB1R16	GCA_002954265.1	2077091	2077091	type	True	76.5153	57	1933	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	76.1861	79	1933	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	76.1716	81	1933	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	75.7702	77	1933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:34,270] [INFO] DFAST Taxonomy check result was written to GCF_003014535.1_ASM301453v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:34,270] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:34,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:34,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfef25dc0-1c36-485b-a3ba-aa097799277d/dqc_reference/checkm_data
[2024-01-25 18:02:34,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:34,328] [INFO] Task started: CheckM
[2024-01-25 18:02:34,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014535.1_ASM301453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014535.1_ASM301453v1_genomic.fna/checkm_input GCF_003014535.1_ASM301453v1_genomic.fna/checkm_result
[2024-01-25 18:03:39,485] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:39,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:39,524] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:39,525] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:39,525] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014535.1_ASM301453v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:39,525] [INFO] Task started: Blastn
[2024-01-25 18:03:39,525] [INFO] Running command: blastn -query GCF_003014535.1_ASM301453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfef25dc0-1c36-485b-a3ba-aa097799277d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014535.1_ASM301453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:40,419] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:40,423] [INFO] Selected 21 target genomes.
[2024-01-25 18:03:40,423] [INFO] Target genome list was writen to GCF_003014535.1_ASM301453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:40,458] [INFO] Task started: fastANI
[2024-01-25 18:03:40,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg63e0d584-fa42-4170-9762-5057bb1239d5/GCF_003014535.1_ASM301453v1_genomic.fna.gz --refList GCF_003014535.1_ASM301453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014535.1_ASM301453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:59,518] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:59,526] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:59,526] [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_003014535.1	s__Edaphocola chishuiensis	100.0	1930	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003545695.1	s__Edaphocola helva	77.6825	405	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545715.1	s__Edaphocola koreensis	77.3664	384	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629695.1	s__Edaphocola lutea	76.9405	147	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168085.1	s__Flavipsychrobacter sp902168085	76.8974	80	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118155.1	s__Edaphocola flava	76.7022	102	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421685.1	s__Flavipsychrobacter sp002421685	76.435	54	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897835.1	s__Flavipsychrobacter sp001897835	76.1589	70	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303395.1	s__Flavipsychrobacter sp017303395	76.0915	59	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786665.1	s__Flavipsychrobacter sp016786665	75.9757	60	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877645.1	s__Flavipsychrobacter sp903877645	75.9618	57	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.60	99.21	0.95	0.89	10	-
GCA_903887005.1	s__Flavipsychrobacter sp903887005	75.3541	52	1933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:59,527] [INFO] GTDB search result was written to GCF_003014535.1_ASM301453v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:59,531] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:59,533] [INFO] DFAST_QC result json was written to GCF_003014535.1_ASM301453v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:59,534] [INFO] DFAST_QC completed!
[2024-01-25 18:03:59,534] [INFO] Total running time: 0h2m9s