[2024-01-24 15:18:34,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:34,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:34,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg726369fb-dd26-4932-906d-e5b2aaa317b7/dqc_reference
[2024-01-24 15:18:38,357] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:38,358] [INFO] Task started: Prodigal
[2024-01-24 15:18:38,359] [INFO] Running command: gunzip -c /var/lib/cwl/stg8852fdbb-41cd-46eb-81ed-1c1cbc7e1e17/GCF_015354735.1_ASM1535473v1_genomic.fna.gz | prodigal -d GCF_015354735.1_ASM1535473v1_genomic.fna/cds.fna -a GCF_015354735.1_ASM1535473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:08,135] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:08,135] [INFO] Task started: HMMsearch
[2024-01-24 15:19:08,135] [INFO] Running command: hmmsearch --tblout GCF_015354735.1_ASM1535473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg726369fb-dd26-4932-906d-e5b2aaa317b7/dqc_reference/reference_markers.hmm GCF_015354735.1_ASM1535473v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:08,520] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:08,522] [INFO] Found 6/6 markers.
[2024-01-24 15:19:08,580] [INFO] Query marker FASTA was written to GCF_015354735.1_ASM1535473v1_genomic.fna/markers.fasta
[2024-01-24 15:19:08,581] [INFO] Task started: Blastn
[2024-01-24 15:19:08,581] [INFO] Running command: blastn -query GCF_015354735.1_ASM1535473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg726369fb-dd26-4932-906d-e5b2aaa317b7/dqc_reference/reference_markers.fasta -out GCF_015354735.1_ASM1535473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:09,231] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:09,234] [INFO] Selected 23 target genomes.
[2024-01-24 15:19:09,235] [INFO] Target genome list was writen to GCF_015354735.1_ASM1535473v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:09,244] [INFO] Task started: fastANI
[2024-01-24 15:19:09,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg8852fdbb-41cd-46eb-81ed-1c1cbc7e1e17/GCF_015354735.1_ASM1535473v1_genomic.fna.gz --refList GCF_015354735.1_ASM1535473v1_genomic.fna/target_genomes.txt --output GCF_015354735.1_ASM1535473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:29,208] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:29,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg726369fb-dd26-4932-906d-e5b2aaa317b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:29,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg726369fb-dd26-4932-906d-e5b2aaa317b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:29,224] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:29,224] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:29,224] [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
Pararhodonellum marinum	strain=SW124	GCA_015354735.1	2755358	2755358	type	True	100.0	1769	1769	95	conclusive
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	77.2357	88	1769	95	below_threshold
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	77.087	96	1769	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	77.0867	99	1769	95	below_threshold
Echinicola arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	76.8467	94	1769	95	below_threshold
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	76.7011	93	1769	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	76.6924	126	1769	95	below_threshold
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	76.532	139	1769	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	76.3906	92	1769	95	below_threshold
Pleomorphovibrio marinus	strain=SW125	GCA_003347495.1	2164132	2164132	type	True	76.3543	93	1769	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	76.3403	95	1769	95	below_threshold
Algoriphagus lutimaris	strain=KCTC 22630	GCA_017051705.1	613197	613197	type	True	76.2123	65	1769	95	below_threshold
Algoriphagus oliviformis	strain=H41	GCA_017254915.1	2811231	2811231	type	True	76.1949	65	1769	95	below_threshold
Algoriphagus mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	76.1544	86	1769	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	76.1282	105	1769	95	below_threshold
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	76.0973	109	1769	95	below_threshold
Algoriphagus locisalis	strain=DSM 23445	GCA_900116615.1	305507	305507	type	True	76.072	68	1769	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	75.9407	71	1769	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:29,226] [INFO] DFAST Taxonomy check result was written to GCF_015354735.1_ASM1535473v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:29,226] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:29,227] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:29,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg726369fb-dd26-4932-906d-e5b2aaa317b7/dqc_reference/checkm_data
[2024-01-24 15:19:29,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:29,289] [INFO] Task started: CheckM
[2024-01-24 15:19:29,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015354735.1_ASM1535473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015354735.1_ASM1535473v1_genomic.fna/checkm_input GCF_015354735.1_ASM1535473v1_genomic.fna/checkm_result
[2024-01-24 15:20:47,794] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:47,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:47,816] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:47,816] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:47,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015354735.1_ASM1535473v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:47,817] [INFO] Task started: Blastn
[2024-01-24 15:20:47,817] [INFO] Running command: blastn -query GCF_015354735.1_ASM1535473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg726369fb-dd26-4932-906d-e5b2aaa317b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_015354735.1_ASM1535473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:48,587] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:48,591] [INFO] Selected 26 target genomes.
[2024-01-24 15:20:48,591] [INFO] Target genome list was writen to GCF_015354735.1_ASM1535473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:48,613] [INFO] Task started: fastANI
[2024-01-24 15:20:48,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg8852fdbb-41cd-46eb-81ed-1c1cbc7e1e17/GCF_015354735.1_ASM1535473v1_genomic.fna.gz --refList GCF_015354735.1_ASM1535473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015354735.1_ASM1535473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:10,219] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:10,249] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:10,250] [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_015354735.1	s__SW124 sp015354735	100.0	1769	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__SW124	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015476655.1	s__Aquiflexum lacus	78.8929	244	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	77.962	225	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637795.1	s__Belliella aquatica	77.087	96	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	76.8944	127	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCF_014841125.1	s__Echinicola sp014841125	76.8467	94	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	76.7011	93	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	76.6924	126	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018500185.1	s__Litoribacter ruber	76.6793	111	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	98.60	98.60	0.91	0.91	2	-
GCF_015533855.1	s__Echinicola sp015533855	76.6257	101	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	76.5475	139	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253485.1	s__Algoriphagus aquaeductus	76.3403	95	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254915.1	s__Algoriphagus sp017254915	76.2508	63	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051705.1	s__Algoriphagus lutimaris	76.2123	65	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429425.1	s__Algoriphagus mannitolivorans	76.1544	86	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002735.1	s__Algoriphagus sp002002735	76.1418	76	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018642165.1	s__Echinicola shivajiensis	76.0973	109	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116615.1	s__Algoriphagus locisalis	76.0716	68	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	75.958	70	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290685.1	s__Cyclobacterium plantarum	75.951	101	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993705.1	s__Cyclobacterium sp010993705	75.804	119	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336015.1	s__Algoriphagus sp018336015	75.5655	79	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:10,252] [INFO] GTDB search result was written to GCF_015354735.1_ASM1535473v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:10,253] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:10,259] [INFO] DFAST_QC result json was written to GCF_015354735.1_ASM1535473v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:10,259] [INFO] DFAST_QC completed!
[2024-01-24 15:21:10,259] [INFO] Total running time: 0h2m36s