[2024-01-24 11:12:54,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:54,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:54,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg51405fe9-d763-4a33-a5e6-2f144b719ce7/dqc_reference
[2024-01-24 11:12:56,283] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:56,284] [INFO] Task started: Prodigal
[2024-01-24 11:12:56,285] [INFO] Running command: gunzip -c /var/lib/cwl/stg928941f3-9bf9-4ec1-83a2-670d8e5a2512/GCF_003347495.1_ASM334749v1_genomic.fna.gz | prodigal -d GCF_003347495.1_ASM334749v1_genomic.fna/cds.fna -a GCF_003347495.1_ASM334749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:28,673] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:28,674] [INFO] Task started: HMMsearch
[2024-01-24 11:13:28,674] [INFO] Running command: hmmsearch --tblout GCF_003347495.1_ASM334749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51405fe9-d763-4a33-a5e6-2f144b719ce7/dqc_reference/reference_markers.hmm GCF_003347495.1_ASM334749v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:29,041] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:29,042] [INFO] Found 6/6 markers.
[2024-01-24 11:13:29,098] [INFO] Query marker FASTA was written to GCF_003347495.1_ASM334749v1_genomic.fna/markers.fasta
[2024-01-24 11:13:29,099] [INFO] Task started: Blastn
[2024-01-24 11:13:29,099] [INFO] Running command: blastn -query GCF_003347495.1_ASM334749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51405fe9-d763-4a33-a5e6-2f144b719ce7/dqc_reference/reference_markers.fasta -out GCF_003347495.1_ASM334749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:29,712] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:29,715] [INFO] Selected 25 target genomes.
[2024-01-24 11:13:29,716] [INFO] Target genome list was writen to GCF_003347495.1_ASM334749v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:29,743] [INFO] Task started: fastANI
[2024-01-24 11:13:29,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg928941f3-9bf9-4ec1-83a2-670d8e5a2512/GCF_003347495.1_ASM334749v1_genomic.fna.gz --refList GCF_003347495.1_ASM334749v1_genomic.fna/target_genomes.txt --output GCF_003347495.1_ASM334749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:52,506] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:52,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51405fe9-d763-4a33-a5e6-2f144b719ce7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:52,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51405fe9-d763-4a33-a5e6-2f144b719ce7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:52,522] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:52,522] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:52,522] [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
Pleomorphovibrio marinus	strain=SW125	GCA_003347495.1	2164132	2164132	type	True	100.0	2088	2091	95	conclusive
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	77.0825	52	2091	95	below_threshold
Lunatimonas lonarensis	strain=AK24	GCA_000390185.1	1232681	1232681	type	True	76.9651	134	2091	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	76.9632	181	2091	95	below_threshold
Cyclobacterium xiamenense	strain=CGMCC 1.12432	GCA_009467825.1	1297121	1297121	type	True	76.7829	132	2091	95	below_threshold
Lunatibacter salilacus	strain=CUG 91308	GCA_009797935.1	2483804	2483804	type	True	76.7162	175	2091	95	below_threshold
Cyclobacterium lianum	strain=CGMCC 1.6102	GCA_900143075.1	388280	388280	type	True	76.702	157	2091	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	76.4562	68	2091	95	below_threshold
Cecembia rubra	strain=DSM 28057	GCA_003014575.1	1485585	1485585	type	True	76.3656	84	2091	95	below_threshold
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	76.3315	81	2091	95	below_threshold
Pararhodonellum marinum	strain=SW124	GCA_015354735.1	2755358	2755358	type	True	76.3116	104	2091	95	below_threshold
Cyclobacterium qasimii	strain=NBRC 106168	GCA_007991695.1	1350429	1350429	type	True	76.1523	100	2091	95	below_threshold
Cyclobacterium qasimii	strain=M12-11B	GCA_000427295.1	1350429	1350429	type	True	76.1083	97	2091	95	below_threshold
Echinicola strongylocentroti	strain=MEBiC08714	GCA_003260975.1	1795355	1795355	type	True	76.0942	80	2091	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	75.9133	101	2091	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	75.792	50	2091	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	75.7486	52	2091	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:52,524] [INFO] DFAST Taxonomy check result was written to GCF_003347495.1_ASM334749v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:52,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:52,525] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:52,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51405fe9-d763-4a33-a5e6-2f144b719ce7/dqc_reference/checkm_data
[2024-01-24 11:13:52,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:52,597] [INFO] Task started: CheckM
[2024-01-24 11:13:52,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003347495.1_ASM334749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003347495.1_ASM334749v1_genomic.fna/checkm_input GCF_003347495.1_ASM334749v1_genomic.fna/checkm_result
[2024-01-24 11:15:17,984] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:17,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:18,004] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:18,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:18,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003347495.1_ASM334749v1_genomic.fna/markers.fasta)
[2024-01-24 11:15:18,005] [INFO] Task started: Blastn
[2024-01-24 11:15:18,006] [INFO] Running command: blastn -query GCF_003347495.1_ASM334749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51405fe9-d763-4a33-a5e6-2f144b719ce7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003347495.1_ASM334749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:18,772] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:18,775] [INFO] Selected 25 target genomes.
[2024-01-24 11:15:18,775] [INFO] Target genome list was writen to GCF_003347495.1_ASM334749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:18,793] [INFO] Task started: fastANI
[2024-01-24 11:15:18,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg928941f3-9bf9-4ec1-83a2-670d8e5a2512/GCF_003347495.1_ASM334749v1_genomic.fna.gz --refList GCF_003347495.1_ASM334749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003347495.1_ASM334749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:41,372] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:41,387] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:41,387] [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_003347495.1	s__Negadavirga sp003347495	100.0	2088	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Negadavirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003565295.1	s__Negadavirga sp003565295	82.1871	778	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Negadavirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993705.1	s__Cyclobacterium sp010993705	77.3126	204	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290685.1	s__Cyclobacterium plantarum	76.9491	182	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762705.1	s__Cyclobacterium sp014762705	76.8845	163	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143075.1	s__Cyclobacterium lianum	76.737	157	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	76.7121	89	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014575.1	s__Cecembia rubra	76.3401	84	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	76.3315	81	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354735.1	s__SW124 sp015354735	76.3116	104	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__SW124	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427295.1	s__Cyclobacterium qasimii	76.1083	97	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	99.96	99.96	0.99	0.99	2	-
GCF_003260975.1	s__Echinicola strongylocentroti	76.0942	80	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	75.9133	101	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373065.1	s__Algoriphagus sp013373065	75.8487	53	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	75.7738	51	2091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:41,390] [INFO] GTDB search result was written to GCF_003347495.1_ASM334749v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:41,391] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:41,397] [INFO] DFAST_QC result json was written to GCF_003347495.1_ASM334749v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:41,397] [INFO] DFAST_QC completed!
[2024-01-24 11:15:41,398] [INFO] Total running time: 0h2m46s