[2024-01-24 12:40:50,396] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:50,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:50,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg60134fb7-50f7-403c-9554-b06638708c54/dqc_reference
[2024-01-24 12:40:51,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:51,611] [INFO] Task started: Prodigal
[2024-01-24 12:40:51,611] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe31036d-e24c-4832-a498-eb2c16a35d53/GCF_009847015.1_ASM984701v1_genomic.fna.gz | prodigal -d GCF_009847015.1_ASM984701v1_genomic.fna/cds.fna -a GCF_009847015.1_ASM984701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:41:15,482] [INFO] Task succeeded: Prodigal
[2024-01-24 12:41:15,482] [INFO] Task started: HMMsearch
[2024-01-24 12:41:15,483] [INFO] Running command: hmmsearch --tblout GCF_009847015.1_ASM984701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60134fb7-50f7-403c-9554-b06638708c54/dqc_reference/reference_markers.hmm GCF_009847015.1_ASM984701v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:41:15,784] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:41:15,786] [INFO] Found 6/6 markers.
[2024-01-24 12:41:15,836] [INFO] Query marker FASTA was written to GCF_009847015.1_ASM984701v1_genomic.fna/markers.fasta
[2024-01-24 12:41:15,836] [INFO] Task started: Blastn
[2024-01-24 12:41:15,836] [INFO] Running command: blastn -query GCF_009847015.1_ASM984701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60134fb7-50f7-403c-9554-b06638708c54/dqc_reference/reference_markers.fasta -out GCF_009847015.1_ASM984701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:16,435] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:16,441] [INFO] Selected 18 target genomes.
[2024-01-24 12:41:16,441] [INFO] Target genome list was writen to GCF_009847015.1_ASM984701v1_genomic.fna/target_genomes.txt
[2024-01-24 12:41:16,465] [INFO] Task started: fastANI
[2024-01-24 12:41:16,465] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe31036d-e24c-4832-a498-eb2c16a35d53/GCF_009847015.1_ASM984701v1_genomic.fna.gz --refList GCF_009847015.1_ASM984701v1_genomic.fna/target_genomes.txt --output GCF_009847015.1_ASM984701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:30,024] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:30,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60134fb7-50f7-403c-9554-b06638708c54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:30,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60134fb7-50f7-403c-9554-b06638708c54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:30,036] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:41:30,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:41:30,037] [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
Sunxiuqinia indica	strain=RC1_OXG_1F	GCA_009847015.1	2692584	2692584	type	True	100.0	1727	1731	95	conclusive
Sunxiuqinia dokdonensis	strain=DH1	GCA_001270965.1	1409788	1409788	type	True	78.5793	409	1731	95	below_threshold
Sunxiuqinia elliptica	strain=CGMCC 1.9156	GCA_900113005.1	655355	655355	type	True	78.0847	350	1731	95	below_threshold
Mangrovibacterium marinum	strain=DSM 28823	GCA_003046625.1	1639118	1639118	type	True	77.5161	165	1731	95	below_threshold
Mangrovibacterium diazotrophicum	strain=DSM 27148	GCA_003610535.1	1261403	1261403	type	True	77.4578	192	1731	95	below_threshold
Mangrovibacterium lignilyticum	strain=BM_7	GCA_010882175.1	2668052	2668052	type	True	77.4245	237	1731	95	below_threshold
Draconibacterium halophilum	strain=M1	GCA_010448835.1	2706887	2706887	type	True	77.0611	132	1731	95	below_threshold
Maribellus sediminis	strain=Y2-1-60	GCA_011799805.1	2696285	2696285	type	True	76.7253	87	1731	95	below_threshold
Mariniphaga anaerophila	strain=DSM 26910	GCA_900129025.1	1484053	1484053	type	True	76.2036	83	1731	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:30,038] [INFO] DFAST Taxonomy check result was written to GCF_009847015.1_ASM984701v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:30,039] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:30,039] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:30,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60134fb7-50f7-403c-9554-b06638708c54/dqc_reference/checkm_data
[2024-01-24 12:41:30,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:30,091] [INFO] Task started: CheckM
[2024-01-24 12:41:30,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009847015.1_ASM984701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009847015.1_ASM984701v1_genomic.fna/checkm_input GCF_009847015.1_ASM984701v1_genomic.fna/checkm_result
[2024-01-24 12:42:38,034] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:38,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:38,062] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:38,062] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:38,062] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009847015.1_ASM984701v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:38,063] [INFO] Task started: Blastn
[2024-01-24 12:42:38,063] [INFO] Running command: blastn -query GCF_009847015.1_ASM984701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60134fb7-50f7-403c-9554-b06638708c54/dqc_reference/reference_markers_gtdb.fasta -out GCF_009847015.1_ASM984701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:38,854] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:38,858] [INFO] Selected 17 target genomes.
[2024-01-24 12:42:38,859] [INFO] Target genome list was writen to GCF_009847015.1_ASM984701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:38,932] [INFO] Task started: fastANI
[2024-01-24 12:42:38,932] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe31036d-e24c-4832-a498-eb2c16a35d53/GCF_009847015.1_ASM984701v1_genomic.fna.gz --refList GCF_009847015.1_ASM984701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009847015.1_ASM984701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:53,025] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:53,040] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:53,040] [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_009847015.1	s__Sunxiuqinia indica	100.0	1727	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Sunxiuqinia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001270965.1	s__Sunxiuqinia dokdonensis	78.5684	410	1731	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	78.1059	348	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Sunxiuqinia	95.0	95.76	95.76	0.90	0.90	3	-
GCF_003046625.1	s__Mangrovibacterium marinum	77.5273	164	1731	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	77.4444	190	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010882175.1	s__Mangrovibacterium sp010882175	77.4371	236	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429385.1	s__UBA6024 sp002429385	76.8979	62	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__UBA6024	95.0	99.95	99.91	0.98	0.98	3	-
GCF_010586825.1	s__Draconibacterium mangrovi	76.7324	131	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011799805.1	s__Draconibacterium sp011799805	76.728	87	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	96.71	96.71	0.85	0.85	2	-
GCF_900129025.1	s__Mariniphaga anaerophila	76.2137	84	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mariniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003506435.1	s__GWE2-42-39 sp003506435	76.1791	107	1731	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_016788685.1	s__UBA6024 sp016788685	75.9994	51	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__UBA6024	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003537645.1	s__UBA6024 sp003537645	75.967	72	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__UBA6024	95.0	97.30	97.30	0.74	0.74	2	-
GCA_018648265.1	s__Draconibacterium sp018648265	75.6759	84	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	99.94	99.92	0.96	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:53,042] [INFO] GTDB search result was written to GCF_009847015.1_ASM984701v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:53,043] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:53,047] [INFO] DFAST_QC result json was written to GCF_009847015.1_ASM984701v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:53,047] [INFO] DFAST_QC completed!
[2024-01-24 12:42:53,047] [INFO] Total running time: 0h2m3s