[2024-01-24 15:02:33,572] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:33,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:33,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg00eefb4c-d554-4bad-9362-ccf5f9cec82e/dqc_reference
[2024-01-24 15:02:34,837] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:34,839] [INFO] Task started: Prodigal
[2024-01-24 15:02:34,839] [INFO] Running command: gunzip -c /var/lib/cwl/stgf69a1750-01be-4ed9-a367-ab4d6106921d/GCF_010882175.1_ASM1088217v1_genomic.fna.gz | prodigal -d GCF_010882175.1_ASM1088217v1_genomic.fna/cds.fna -a GCF_010882175.1_ASM1088217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:04,012] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:04,012] [INFO] Task started: HMMsearch
[2024-01-24 15:03:04,013] [INFO] Running command: hmmsearch --tblout GCF_010882175.1_ASM1088217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00eefb4c-d554-4bad-9362-ccf5f9cec82e/dqc_reference/reference_markers.hmm GCF_010882175.1_ASM1088217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:04,375] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:04,377] [INFO] Found 6/6 markers.
[2024-01-24 15:03:04,422] [INFO] Query marker FASTA was written to GCF_010882175.1_ASM1088217v1_genomic.fna/markers.fasta
[2024-01-24 15:03:04,423] [INFO] Task started: Blastn
[2024-01-24 15:03:04,423] [INFO] Running command: blastn -query GCF_010882175.1_ASM1088217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00eefb4c-d554-4bad-9362-ccf5f9cec82e/dqc_reference/reference_markers.fasta -out GCF_010882175.1_ASM1088217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:05,155] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:05,159] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:05,159] [INFO] Target genome list was writen to GCF_010882175.1_ASM1088217v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:05,170] [INFO] Task started: fastANI
[2024-01-24 15:03:05,171] [INFO] Running command: fastANI --query /var/lib/cwl/stgf69a1750-01be-4ed9-a367-ab4d6106921d/GCF_010882175.1_ASM1088217v1_genomic.fna.gz --refList GCF_010882175.1_ASM1088217v1_genomic.fna/target_genomes.txt --output GCF_010882175.1_ASM1088217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:18,583] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:18,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00eefb4c-d554-4bad-9362-ccf5f9cec82e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:18,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00eefb4c-d554-4bad-9362-ccf5f9cec82e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:18,594] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:18,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:18,594] [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
Mangrovibacterium lignilyticum	strain=BM_7	GCA_010882175.1	2668052	2668052	type	True	100.0	1867	1869	95	conclusive
Mangrovibacterium marinum	strain=DSM 28823	GCA_003046625.1	1639118	1639118	type	True	79.9726	533	1869	95	below_threshold
Mangrovibacterium diazotrophicum	strain=DSM 27148	GCA_003610535.1	1261403	1261403	type	True	79.8002	822	1869	95	below_threshold
Sunxiuqinia indica	strain=RC1_OXG_1F	GCA_009847015.1	2692584	2692584	type	True	77.5528	232	1869	95	below_threshold
Sunxiuqinia elliptica	strain=CGMCC 1.9156	GCA_900113005.1	655355	655355	type	True	77.1989	166	1869	95	below_threshold
Sunxiuqinia dokdonensis	strain=DH1	GCA_001270965.1	1409788	1409788	type	True	76.8481	178	1869	95	below_threshold
Draconibacterium sediminis	strain=JN14CK-3	GCA_000949475.1	1544798	1544798	type	True	76.689	115	1869	95	below_threshold
Draconibacterium orientale	strain=FH5	GCA_000626635.1	1168034	1168034	type	True	76.5809	131	1869	95	below_threshold
Draconibacterium orientale	strain=DSM 25947	GCA_900111425.1	1168034	1168034	type	True	76.5787	130	1869	95	below_threshold
Maribellus sediminis	strain=Y2-1-60	GCA_011799805.1	2696285	2696285	type	True	76.5512	110	1869	95	below_threshold
Carboxylicivirga linearis	strain=FB218	GCA_018271995.1	1628157	1628157	type	True	76.0651	50	1869	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:18,596] [INFO] DFAST Taxonomy check result was written to GCF_010882175.1_ASM1088217v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:18,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:18,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:18,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00eefb4c-d554-4bad-9362-ccf5f9cec82e/dqc_reference/checkm_data
[2024-01-24 15:03:18,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:18,655] [INFO] Task started: CheckM
[2024-01-24 15:03:18,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010882175.1_ASM1088217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010882175.1_ASM1088217v1_genomic.fna/checkm_input GCF_010882175.1_ASM1088217v1_genomic.fna/checkm_result
[2024-01-24 15:04:39,110] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:39,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:39,138] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:39,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:39,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010882175.1_ASM1088217v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:39,139] [INFO] Task started: Blastn
[2024-01-24 15:04:39,139] [INFO] Running command: blastn -query GCF_010882175.1_ASM1088217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00eefb4c-d554-4bad-9362-ccf5f9cec82e/dqc_reference/reference_markers_gtdb.fasta -out GCF_010882175.1_ASM1088217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:40,070] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:40,074] [INFO] Selected 18 target genomes.
[2024-01-24 15:04:40,074] [INFO] Target genome list was writen to GCF_010882175.1_ASM1088217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:40,091] [INFO] Task started: fastANI
[2024-01-24 15:04:40,092] [INFO] Running command: fastANI --query /var/lib/cwl/stgf69a1750-01be-4ed9-a367-ab4d6106921d/GCF_010882175.1_ASM1088217v1_genomic.fna.gz --refList GCF_010882175.1_ASM1088217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010882175.1_ASM1088217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:55,035] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:55,047] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:55,047] [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_010882175.1	s__Mangrovibacterium sp010882175	100.0	1867	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003046625.1	s__Mangrovibacterium marinum	79.9818	532	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610535.1	s__Mangrovibacterium diazotrophicum	79.7998	820	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003246935.1	s__Mangrovibacterium sp003246935	79.1617	423	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009847015.1	s__Sunxiuqinia indica	77.5548	231	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Sunxiuqinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113005.1	s__Sunxiuqinia elliptica	77.2167	164	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Sunxiuqinia	95.0	95.76	95.76	0.90	0.90	3	-
GCF_010586825.1	s__Draconibacterium mangrovi	76.8671	130	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270965.1	s__Sunxiuqinia dokdonensis	76.8481	178	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Sunxiuqinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011799805.1	s__Draconibacterium sp011799805	76.5512	110	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	96.71	96.71	0.85	0.85	2	-
GCA_002429385.1	s__UBA6024 sp002429385	76.418	68	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__UBA6024	95.0	99.95	99.91	0.98	0.98	3	-
GCA_016788685.1	s__UBA6024 sp016788685	76.0948	65	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__UBA6024	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018271995.1	s__Carboxylicivirga linearis	76.0823	51	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019163175.1	s__UBA6024 sp019163175	75.9786	97	1869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__UBA6024	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:55,054] [INFO] GTDB search result was written to GCF_010882175.1_ASM1088217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:55,055] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:55,059] [INFO] DFAST_QC result json was written to GCF_010882175.1_ASM1088217v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:55,059] [INFO] DFAST_QC completed!
[2024-01-24 15:04:55,059] [INFO] Total running time: 0h2m21s