[2024-01-24 11:34:54,992] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:54,995] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:54,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg77a3013e-ef3c-4250-872a-925c8a221ada/dqc_reference
[2024-01-24 11:34:56,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,558] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,559] [INFO] Running command: gunzip -c /var/lib/cwl/stg335c457f-07ce-4a63-aa26-b6b96ba570b9/GCF_014652135.1_ASM1465213v1_genomic.fna.gz | prodigal -d GCF_014652135.1_ASM1465213v1_genomic.fna/cds.fna -a GCF_014652135.1_ASM1465213v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:17,342] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:17,343] [INFO] Task started: HMMsearch
[2024-01-24 11:35:17,343] [INFO] Running command: hmmsearch --tblout GCF_014652135.1_ASM1465213v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77a3013e-ef3c-4250-872a-925c8a221ada/dqc_reference/reference_markers.hmm GCF_014652135.1_ASM1465213v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:17,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:17,641] [INFO] Found 6/6 markers.
[2024-01-24 11:35:17,685] [INFO] Query marker FASTA was written to GCF_014652135.1_ASM1465213v1_genomic.fna/markers.fasta
[2024-01-24 11:35:17,686] [INFO] Task started: Blastn
[2024-01-24 11:35:17,687] [INFO] Running command: blastn -query GCF_014652135.1_ASM1465213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77a3013e-ef3c-4250-872a-925c8a221ada/dqc_reference/reference_markers.fasta -out GCF_014652135.1_ASM1465213v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:18,302] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:18,306] [INFO] Selected 17 target genomes.
[2024-01-24 11:35:18,306] [INFO] Target genome list was writen to GCF_014652135.1_ASM1465213v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:18,313] [INFO] Task started: fastANI
[2024-01-24 11:35:18,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg335c457f-07ce-4a63-aa26-b6b96ba570b9/GCF_014652135.1_ASM1465213v1_genomic.fna.gz --refList GCF_014652135.1_ASM1465213v1_genomic.fna/target_genomes.txt --output GCF_014652135.1_ASM1465213v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:32,038] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:32,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77a3013e-ef3c-4250-872a-925c8a221ada/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:32,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77a3013e-ef3c-4250-872a-925c8a221ada/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:32,052] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:32,052] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:32,052] [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
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	100.0	1463	1464	95	conclusive
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	83.9264	909	1464	95	below_threshold
Cecembia rubra	strain=DSM 28057	GCA_003014575.1	1485585	1485585	type	True	77.9023	241	1464	95	below_threshold
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	77.6762	184	1464	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	77.3921	196	1464	95	below_threshold
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	77.2615	193	1464	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	77.1413	70	1464	95	below_threshold
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	77.057	192	1464	95	below_threshold
Algoriphagus mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	77.0178	106	1464	95	below_threshold
Algoriphagus boseongensis	strain=CECT 8446	GCA_004362805.1	1442587	1442587	type	True	76.9208	123	1464	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	76.7991	136	1464	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	76.7464	110	1464	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	76.7365	81	1464	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	76.7188	85	1464	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	76.5314	191	1464	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	76.46	171	1464	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:32,054] [INFO] DFAST Taxonomy check result was written to GCF_014652135.1_ASM1465213v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:32,055] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:32,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:32,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77a3013e-ef3c-4250-872a-925c8a221ada/dqc_reference/checkm_data
[2024-01-24 11:35:32,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:32,097] [INFO] Task started: CheckM
[2024-01-24 11:35:32,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652135.1_ASM1465213v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652135.1_ASM1465213v1_genomic.fna/checkm_input GCF_014652135.1_ASM1465213v1_genomic.fna/checkm_result
[2024-01-24 11:36:32,410] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:32,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:32,433] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:32,433] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:32,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652135.1_ASM1465213v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:32,434] [INFO] Task started: Blastn
[2024-01-24 11:36:32,434] [INFO] Running command: blastn -query GCF_014652135.1_ASM1465213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77a3013e-ef3c-4250-872a-925c8a221ada/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652135.1_ASM1465213v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:33,243] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:33,248] [INFO] Selected 20 target genomes.
[2024-01-24 11:36:33,248] [INFO] Target genome list was writen to GCF_014652135.1_ASM1465213v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:33,263] [INFO] Task started: fastANI
[2024-01-24 11:36:33,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg335c457f-07ce-4a63-aa26-b6b96ba570b9/GCF_014652135.1_ASM1465213v1_genomic.fna.gz --refList GCF_014652135.1_ASM1465213v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652135.1_ASM1465213v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:49,105] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:49,126] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:49,127] [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_014652135.1	s__Mongoliitalea lutea	100.0	1463	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000298295.1	s__Cecembia lonarensis	79.0086	264	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	78.6778	194	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCF_004216715.1	s__Cecembia calidifontis	78.5105	232	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156785.1	s__Belliella pelovolcani	78.3183	205	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265405.1	s__Belliella baltica	77.6762	184	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	77.6453	214	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637795.1	s__Belliella aquatica	77.2474	194	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429445.1	s__Algoriphagus terrigena	77.1051	71	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	77.0312	194	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429425.1	s__Algoriphagus mannitolivorans	77.0178	106	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362805.1	s__Algoriphagus boseongensis	76.921	122	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	76.9144	216	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007655305.1	s__Algoriphagus sp007655305	76.7991	136	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003797895.1	s__Cecembia sp003797895	76.7955	197	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	76.7477	111	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	76.7188	85	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	76.5212	192	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	76.4701	78	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316845.1	s__Aquiflexum_A aquatile	76.4594	171	1464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:49,129] [INFO] GTDB search result was written to GCF_014652135.1_ASM1465213v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:49,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:49,133] [INFO] DFAST_QC result json was written to GCF_014652135.1_ASM1465213v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:49,133] [INFO] DFAST_QC completed!
[2024-01-24 11:36:49,133] [INFO] Total running time: 0h1m54s