[2024-01-25 17:49:20,476] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:20,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:20,478] [INFO] DQC Reference Directory: /var/lib/cwl/stg68af1334-5396-43ee-b8ff-6f84bdfe541c/dqc_reference
[2024-01-25 17:49:21,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:21,634] [INFO] Task started: Prodigal
[2024-01-25 17:49:21,634] [INFO] Running command: gunzip -c /var/lib/cwl/stge87e3cab-b80e-427d-8af0-8622f2027495/GCF_003014575.1_ASM301457v1_genomic.fna.gz | prodigal -d GCF_003014575.1_ASM301457v1_genomic.fna/cds.fna -a GCF_003014575.1_ASM301457v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:39,985] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:39,985] [INFO] Task started: HMMsearch
[2024-01-25 17:49:39,986] [INFO] Running command: hmmsearch --tblout GCF_003014575.1_ASM301457v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68af1334-5396-43ee-b8ff-6f84bdfe541c/dqc_reference/reference_markers.hmm GCF_003014575.1_ASM301457v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:40,247] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:40,248] [INFO] Found 6/6 markers.
[2024-01-25 17:49:40,286] [INFO] Query marker FASTA was written to GCF_003014575.1_ASM301457v1_genomic.fna/markers.fasta
[2024-01-25 17:49:40,286] [INFO] Task started: Blastn
[2024-01-25 17:49:40,286] [INFO] Running command: blastn -query GCF_003014575.1_ASM301457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68af1334-5396-43ee-b8ff-6f84bdfe541c/dqc_reference/reference_markers.fasta -out GCF_003014575.1_ASM301457v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:40,838] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:40,842] [INFO] Selected 19 target genomes.
[2024-01-25 17:49:40,842] [INFO] Target genome list was writen to GCF_003014575.1_ASM301457v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:40,865] [INFO] Task started: fastANI
[2024-01-25 17:49:40,865] [INFO] Running command: fastANI --query /var/lib/cwl/stge87e3cab-b80e-427d-8af0-8622f2027495/GCF_003014575.1_ASM301457v1_genomic.fna.gz --refList GCF_003014575.1_ASM301457v1_genomic.fna/target_genomes.txt --output GCF_003014575.1_ASM301457v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:57,179] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:57,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68af1334-5396-43ee-b8ff-6f84bdfe541c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:57,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68af1334-5396-43ee-b8ff-6f84bdfe541c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:57,190] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:49:57,190] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:57,190] [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
Cecembia rubra	strain=DSM 28057	GCA_003014575.1	1485585	1485585	type	True	100.0	1565	1567	95	conclusive
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	82.7585	1038	1567	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	79.8554	585	1567	95	below_threshold
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	77.9025	197	1567	95	below_threshold
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	77.8442	254	1567	95	below_threshold
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	77.5105	322	1567	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	77.1901	165	1567	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	77.0324	281	1567	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	76.9197	248	1567	95	below_threshold
Algoriphagus formosus	strain=XAY3209	GCA_002807035.1	2007308	2007308	type	True	76.8992	101	1567	95	below_threshold
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	76.8349	76	1567	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	76.7726	169	1567	95	below_threshold
Algoriphagus marincola	strain=DSM 16067	GCA_000429405.1	264027	264027	type	True	76.6538	95	1567	95	below_threshold
Algoriphagus aquimaris	strain=F21	GCA_004358035.1	2547398	2547398	type	True	76.6367	101	1567	95	below_threshold
Rhodonellum psychrophilum	strain=GCM71	GCA_000473765.1	336828	336828	type	True	76.5572	170	1567	95	below_threshold
Rhodonellum psychrophilum	strain=DSM 17998	GCA_000381545.1	336828	336828	type	True	76.557	173	1567	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	76.5399	115	1567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:57,192] [INFO] DFAST Taxonomy check result was written to GCF_003014575.1_ASM301457v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:57,193] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:57,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:57,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68af1334-5396-43ee-b8ff-6f84bdfe541c/dqc_reference/checkm_data
[2024-01-25 17:49:57,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:57,242] [INFO] Task started: CheckM
[2024-01-25 17:49:57,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014575.1_ASM301457v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014575.1_ASM301457v1_genomic.fna/checkm_input GCF_003014575.1_ASM301457v1_genomic.fna/checkm_result
[2024-01-25 17:50:50,567] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:50,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:50,597] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:50,597] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:50,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014575.1_ASM301457v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:50,599] [INFO] Task started: Blastn
[2024-01-25 17:50:50,599] [INFO] Running command: blastn -query GCF_003014575.1_ASM301457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68af1334-5396-43ee-b8ff-6f84bdfe541c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014575.1_ASM301457v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:51,387] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:51,391] [INFO] Selected 17 target genomes.
[2024-01-25 17:50:51,391] [INFO] Target genome list was writen to GCF_003014575.1_ASM301457v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:51,406] [INFO] Task started: fastANI
[2024-01-25 17:50:51,406] [INFO] Running command: fastANI --query /var/lib/cwl/stge87e3cab-b80e-427d-8af0-8622f2027495/GCF_003014575.1_ASM301457v1_genomic.fna.gz --refList GCF_003014575.1_ASM301457v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014575.1_ASM301457v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:06,906] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:06,916] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:06,917] [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_003014575.1	s__Cecembia rubra	100.0	1565	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004216715.1	s__Cecembia calidifontis	82.7507	1039	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	79.8665	584	1567	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	78.8853	429	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCA_014762705.1	s__Cyclobacterium sp014762705	78.3117	123	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	78.1117	296	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	77.8393	255	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003797895.1	s__Cecembia sp003797895	77.6986	410	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	77.482	327	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807035.1	s__Algoriphagus formosus	76.8992	101	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.55	97.55	0.93	0.93	2	-
GCF_017254835.1	s__Algoriphagus aestuariicola	76.8349	76	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637795.1	s__Belliella aquatica	76.7554	169	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429405.1	s__Algoriphagus marincola	76.6538	95	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.35	97.35	0.90	0.90	2	-
GCF_000526355.1	s__Algoriphagus marincola_A	76.6257	97	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000381545.1	s__Rhodonellum psychrophilum	76.557	173	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Rhodonellum	95.0	99.99	99.99	1.00	0.99	3	-
GCF_003583985.1	s__Algoriphagus lacus	76.5399	115	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124425.1	s__Lunatimonas sp016124425	76.2265	55	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:06,918] [INFO] GTDB search result was written to GCF_003014575.1_ASM301457v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:06,918] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:06,921] [INFO] DFAST_QC result json was written to GCF_003014575.1_ASM301457v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:06,921] [INFO] DFAST_QC completed!
[2024-01-25 17:51:06,921] [INFO] Total running time: 0h1m46s