[2024-01-24 11:51:50,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:50,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:50,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf5bd6cb-c6e1-4901-86c8-9731d073996a/dqc_reference
[2024-01-24 11:51:51,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,699] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,699] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f5cf684-279f-4293-b455-0065968a59a9/GCF_010671565.1_ASM1067156v1_genomic.fna.gz | prodigal -d GCF_010671565.1_ASM1067156v1_genomic.fna/cds.fna -a GCF_010671565.1_ASM1067156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:06,218] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:06,219] [INFO] Task started: HMMsearch
[2024-01-24 11:52:06,219] [INFO] Running command: hmmsearch --tblout GCF_010671565.1_ASM1067156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf5bd6cb-c6e1-4901-86c8-9731d073996a/dqc_reference/reference_markers.hmm GCF_010671565.1_ASM1067156v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:06,472] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:06,474] [INFO] Found 6/6 markers.
[2024-01-24 11:52:06,514] [INFO] Query marker FASTA was written to GCF_010671565.1_ASM1067156v1_genomic.fna/markers.fasta
[2024-01-24 11:52:06,515] [INFO] Task started: Blastn
[2024-01-24 11:52:06,515] [INFO] Running command: blastn -query GCF_010671565.1_ASM1067156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf5bd6cb-c6e1-4901-86c8-9731d073996a/dqc_reference/reference_markers.fasta -out GCF_010671565.1_ASM1067156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:07,171] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:07,174] [INFO] Selected 29 target genomes.
[2024-01-24 11:52:07,174] [INFO] Target genome list was writen to GCF_010671565.1_ASM1067156v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:07,186] [INFO] Task started: fastANI
[2024-01-24 11:52:07,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f5cf684-279f-4293-b455-0065968a59a9/GCF_010671565.1_ASM1067156v1_genomic.fna.gz --refList GCF_010671565.1_ASM1067156v1_genomic.fna/target_genomes.txt --output GCF_010671565.1_ASM1067156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:23,665] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:23,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf5bd6cb-c6e1-4901-86c8-9731d073996a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:23,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf5bd6cb-c6e1-4901-86c8-9731d073996a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:23,697] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:23,697] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:23,698] [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
Spongiivirga citrea	strain=KCTC 32990	GCA_010671565.1	1481457	1481457	type	True	100.0	1370	1373	95	conclusive
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	77.448	94	1373	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.1937	100	1373	95	below_threshold
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	77.1692	82	1373	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.0944	86	1373	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.0936	97	1373	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.0581	108	1373	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.0552	108	1373	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.9148	96	1373	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	76.801	104	1373	95	below_threshold
Kordia zhangzhouensis	strain=MCCC 1A00726	GCA_001005305.1	1620405	1620405	type	True	76.7258	81	1373	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.6916	90	1373	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.6816	100	1373	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.6636	93	1373	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	76.6146	103	1373	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	76.5808	106	1373	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	76.5426	87	1373	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.5216	90	1373	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	76.521	90	1373	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.5189	98	1373	95	below_threshold
Algibacter onchidii	strain=XY-114	GCA_004804355.1	2562860	2562860	type	True	76.4849	86	1373	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.4752	102	1373	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.4427	100	1373	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.4216	106	1373	95	below_threshold
Aestuariibaculum sediminum	strain=TT11	GCA_014596945.1	2770637	2770637	type	True	76.3203	92	1373	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.293	97	1373	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	76.281	77	1373	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	75.9158	79	1373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:23,699] [INFO] DFAST Taxonomy check result was written to GCF_010671565.1_ASM1067156v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:23,701] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:23,701] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:23,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf5bd6cb-c6e1-4901-86c8-9731d073996a/dqc_reference/checkm_data
[2024-01-24 11:52:23,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:23,747] [INFO] Task started: CheckM
[2024-01-24 11:52:23,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010671565.1_ASM1067156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010671565.1_ASM1067156v1_genomic.fna/checkm_input GCF_010671565.1_ASM1067156v1_genomic.fna/checkm_result
[2024-01-24 11:53:07,880] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:07,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:07,907] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:07,907] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:07,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010671565.1_ASM1067156v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:07,908] [INFO] Task started: Blastn
[2024-01-24 11:53:07,908] [INFO] Running command: blastn -query GCF_010671565.1_ASM1067156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf5bd6cb-c6e1-4901-86c8-9731d073996a/dqc_reference/reference_markers_gtdb.fasta -out GCF_010671565.1_ASM1067156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:08,782] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:08,786] [INFO] Selected 29 target genomes.
[2024-01-24 11:53:08,787] [INFO] Target genome list was writen to GCF_010671565.1_ASM1067156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:08,824] [INFO] Task started: fastANI
[2024-01-24 11:53:08,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f5cf684-279f-4293-b455-0065968a59a9/GCF_010671565.1_ASM1067156v1_genomic.fna.gz --refList GCF_010671565.1_ASM1067156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010671565.1_ASM1067156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:26,337] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:26,366] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:26,366] [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_010671565.1	s__Spongiivirga citrea	100.0	1370	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Spongiivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000723205.1	s__Formosa agariphila	77.1692	82	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	77.1131	96	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	77.0792	107	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003335675.1	s__Winogradskyella sp003335675	77.0783	74	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	76.9407	95	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163855.1	s__Winogradskyella sp002163855	76.9234	105	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCF_004310325.1	s__Jejuia sp004310325	76.7928	93	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	76.7809	115	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	76.7024	99	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	76.6952	115	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004310335.1	s__Jejuia pacifica	76.6576	91	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011777505.1	s__CAU-1491 sp011777505	76.6245	91	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709615.1	s__Winogradskyella ouciana	76.6146	103	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCA_016744415.1	s__Urechidicola sp016744415	76.5936	66	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642835.1	s__Tamlana_A agarivorans	76.5426	87	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	95.46	95.44	0.83	0.81	3	-
GCF_004804355.1	s__Tamlana_C sp004804355	76.4849	86	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	76.4597	100	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	76.4407	131	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009901575.1	s__Leptobacterium sp009901575	76.4228	97	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635865.1	s__Winogradskyella haliclonae	76.4216	106	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	76.4153	129	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425305.1	s__Psychroserpens burtonensis	76.3569	84	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
GCF_014596945.1	s__Aestuariibaculum sediminum	76.3416	91	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144745.1	s__Croceivirga sp005144745	76.3181	58	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.80	97.80	0.93	0.93	2	-
GCF_008056315.1	s__Seonamhaeicola maritimus	76.293	97	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	76.2523	96	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993855.1	s__Muricauda sp010993855	76.1871	79	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211785.1	s__Winogradskyella sp004211785	76.1561	80	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:26,368] [INFO] GTDB search result was written to GCF_010671565.1_ASM1067156v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:26,368] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:26,373] [INFO] DFAST_QC result json was written to GCF_010671565.1_ASM1067156v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:26,373] [INFO] DFAST_QC completed!
[2024-01-24 11:53:26,374] [INFO] Total running time: 0h1m36s