[2024-01-24 12:45:10,144] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,151] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,151] [INFO] DQC Reference Directory: /var/lib/cwl/stgbda29580-72f5-4dd7-878d-03a936d9f645/dqc_reference
[2024-01-24 12:45:13,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,084] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,085] [INFO] Running command: gunzip -c /var/lib/cwl/stgacc5ec47-ceec-49b5-ab98-4fbd94ea97a0/GCF_003573545.1_ASM357354v1_genomic.fna.gz | prodigal -d GCF_003573545.1_ASM357354v1_genomic.fna/cds.fna -a GCF_003573545.1_ASM357354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:40,078] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:40,079] [INFO] Task started: HMMsearch
[2024-01-24 12:45:40,079] [INFO] Running command: hmmsearch --tblout GCF_003573545.1_ASM357354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbda29580-72f5-4dd7-878d-03a936d9f645/dqc_reference/reference_markers.hmm GCF_003573545.1_ASM357354v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:40,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:40,400] [INFO] Found 6/6 markers.
[2024-01-24 12:45:40,913] [INFO] Query marker FASTA was written to GCF_003573545.1_ASM357354v1_genomic.fna/markers.fasta
[2024-01-24 12:45:40,914] [INFO] Task started: Blastn
[2024-01-24 12:45:40,914] [INFO] Running command: blastn -query GCF_003573545.1_ASM357354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbda29580-72f5-4dd7-878d-03a936d9f645/dqc_reference/reference_markers.fasta -out GCF_003573545.1_ASM357354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:41,538] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:41,542] [INFO] Selected 17 target genomes.
[2024-01-24 12:45:41,542] [INFO] Target genome list was writen to GCF_003573545.1_ASM357354v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:41,552] [INFO] Task started: fastANI
[2024-01-24 12:45:41,552] [INFO] Running command: fastANI --query /var/lib/cwl/stgacc5ec47-ceec-49b5-ab98-4fbd94ea97a0/GCF_003573545.1_ASM357354v1_genomic.fna.gz --refList GCF_003573545.1_ASM357354v1_genomic.fna/target_genomes.txt --output GCF_003573545.1_ASM357354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:56,615] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:56,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbda29580-72f5-4dd7-878d-03a936d9f645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:56,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbda29580-72f5-4dd7-878d-03a936d9f645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:56,626] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:56,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:56,627] [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
Mariniphaga sediminis	strain=SY21	GCA_003573545.1	1628158	1628158	type	True	100.0	1884	1908	95	conclusive
Mariniphaga anaerophila	strain=DSM 26910	GCA_900129025.1	1484053	1484053	type	True	77.8318	385	1908	95	below_threshold
Maribellus luteus	strain=XSD2	GCA_003576475.1	2305463	2305463	type	True	77.4318	192	1908	95	below_threshold
Maribellus comscasis	strain=WC007	GCA_009762775.1	2681766	2681766	type	True	77.006	231	1908	95	below_threshold
Tangfeifania diversioriginum	strain=DSM 27063	GCA_900141875.1	1168035	1168035	type	True	76.9325	330	1908	95	below_threshold
Maribellus maritimus	strain=5E3	GCA_022267315.1	2870838	2870838	type	True	76.9298	221	1908	95	below_threshold
Sunxiuqinia elliptica	strain=CGMCC 1.9156	GCA_900113005.1	655355	655355	type	True	76.4625	57	1908	95	below_threshold
Draconibacterium sediminis	strain=JN14CK-3	GCA_000949475.1	1544798	1544798	type	True	76.3064	145	1908	95	below_threshold
Maribellus sediminis	strain=Y2-1-60	GCA_011799805.1	2696285	2696285	type	True	76.2666	134	1908	95	below_threshold
Draconibacterium mangrovi	strain=GM2-18	GCA_010586825.1	2697469	2697469	type	True	76.2529	150	1908	95	below_threshold
Sunxiuqinia dokdonensis	strain=DH1	GCA_001270965.1	1409788	1409788	type	True	75.7966	78	1908	95	below_threshold
Mangrovibacterium marinum	strain=DSM 28823	GCA_003046625.1	1639118	1639118	type	True	75.4422	54	1908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:56,631] [INFO] DFAST Taxonomy check result was written to GCF_003573545.1_ASM357354v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:56,632] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:56,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:56,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbda29580-72f5-4dd7-878d-03a936d9f645/dqc_reference/checkm_data
[2024-01-24 12:45:56,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:56,692] [INFO] Task started: CheckM
[2024-01-24 12:45:56,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003573545.1_ASM357354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003573545.1_ASM357354v1_genomic.fna/checkm_input GCF_003573545.1_ASM357354v1_genomic.fna/checkm_result
[2024-01-24 12:47:10,348] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:10,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:10,372] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:10,373] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:10,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003573545.1_ASM357354v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:10,374] [INFO] Task started: Blastn
[2024-01-24 12:47:10,374] [INFO] Running command: blastn -query GCF_003573545.1_ASM357354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbda29580-72f5-4dd7-878d-03a936d9f645/dqc_reference/reference_markers_gtdb.fasta -out GCF_003573545.1_ASM357354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:11,170] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:11,175] [INFO] Selected 18 target genomes.
[2024-01-24 12:47:11,176] [INFO] Target genome list was writen to GCF_003573545.1_ASM357354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:11,713] [INFO] Task started: fastANI
[2024-01-24 12:47:11,713] [INFO] Running command: fastANI --query /var/lib/cwl/stgacc5ec47-ceec-49b5-ab98-4fbd94ea97a0/GCF_003573545.1_ASM357354v1_genomic.fna.gz --refList GCF_003573545.1_ASM357354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003573545.1_ASM357354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:27,055] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:27,074] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:27,074] [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_003573545.1	s__Mariniphaga sediminis	100.0	1885	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mariniphaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129025.1	s__Mariniphaga anaerophila	77.8311	385	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mariniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576475.1	s__Draconibacterium luteum	77.4318	192	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762775.1	s__Draconibacterium comscasis	77.0247	231	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141875.1	s__Tangfeifania diversioriginum	76.9395	328	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Tangfeifania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016930735.1	s__JABMQB01 sp016930735	76.3684	88	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__JABMQB01	95.0	99.46	99.46	0.82	0.82	2	-
GCF_000949475.1	s__Draconibacterium sediminis	76.3322	143	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931875.1	s__Draconibacterium sp016931875	76.3208	148	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018648265.1	s__Draconibacterium sp018648265	76.2872	137	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	99.94	99.92	0.96	0.95	4	-
GCF_011799805.1	s__Draconibacterium sp011799805	76.2465	138	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	96.71	96.71	0.85	0.85	2	-
GCF_010586825.1	s__Draconibacterium mangrovi	76.2376	150	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773765.1	s__Draconibacterium sp009773765	76.2046	136	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705335.1	s__Draconibacterium sp016705335	76.1363	135	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003506435.1	s__GWE2-42-39 sp003506435	76.0727	86	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__GWE2-42-39	95.0	99.97	99.92	0.99	0.98	6	-
GCA_018400515.1	s__Tangfeifania sp018400515	76.0662	97	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Tangfeifania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015493625.1	s__Draconibacterium sp015493625	75.9759	71	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:27,076] [INFO] GTDB search result was written to GCF_003573545.1_ASM357354v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:27,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:27,081] [INFO] DFAST_QC result json was written to GCF_003573545.1_ASM357354v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:27,082] [INFO] DFAST_QC completed!
[2024-01-24 12:47:27,082] [INFO] Total running time: 0h2m17s