[2024-01-25 17:43:51,007] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:51,010] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:51,010] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb367178-0543-4cf1-910b-50907312b875/dqc_reference
[2024-01-25 17:43:52,117] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:52,118] [INFO] Task started: Prodigal
[2024-01-25 17:43:52,118] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4c5d076-ecf6-4965-8164-c135be8bf545/GCF_022760175.1_ASM2276017v1_genomic.fna.gz | prodigal -d GCF_022760175.1_ASM2276017v1_genomic.fna/cds.fna -a GCF_022760175.1_ASM2276017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:04,954] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:04,954] [INFO] Task started: HMMsearch
[2024-01-25 17:44:04,954] [INFO] Running command: hmmsearch --tblout GCF_022760175.1_ASM2276017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb367178-0543-4cf1-910b-50907312b875/dqc_reference/reference_markers.hmm GCF_022760175.1_ASM2276017v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:05,244] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:05,245] [INFO] Found 6/6 markers.
[2024-01-25 17:44:05,278] [INFO] Query marker FASTA was written to GCF_022760175.1_ASM2276017v1_genomic.fna/markers.fasta
[2024-01-25 17:44:05,279] [INFO] Task started: Blastn
[2024-01-25 17:44:05,279] [INFO] Running command: blastn -query GCF_022760175.1_ASM2276017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb367178-0543-4cf1-910b-50907312b875/dqc_reference/reference_markers.fasta -out GCF_022760175.1_ASM2276017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:05,955] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:05,958] [INFO] Selected 22 target genomes.
[2024-01-25 17:44:05,958] [INFO] Target genome list was writen to GCF_022760175.1_ASM2276017v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:05,989] [INFO] Task started: fastANI
[2024-01-25 17:44:05,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4c5d076-ecf6-4965-8164-c135be8bf545/GCF_022760175.1_ASM2276017v1_genomic.fna.gz --refList GCF_022760175.1_ASM2276017v1_genomic.fna/target_genomes.txt --output GCF_022760175.1_ASM2276017v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:20,876] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:20,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb367178-0543-4cf1-910b-50907312b875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:20,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb367178-0543-4cf1-910b-50907312b875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:20,888] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:44:20,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:20,888] [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
Zhouia spongiae	strain=HN-Y44	GCA_022760175.1	2202721	2202721	type	True	100.0	1345	1346	95	conclusive
Zhouia amylolytica	strain=CGMCC 1.6114	GCA_900116365.1	376730	376730	type	True	79.6869	520	1346	95	below_threshold
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	77.1249	79	1346	95	below_threshold
Imtechella halotolerans	strain=K1	GCA_000260835.1	1165090	1165090	type	True	77.1061	85	1346	95	below_threshold
Galbibacter marinus	strain=ck-I2-15	GCA_000300875.1	555500	555500	type	True	77.0311	86	1346	95	below_threshold
Robertkochia marina	strain=CC-AMO-30D	GCA_007279605.1	1227945	1227945	type	True	76.9137	86	1346	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	76.8613	60	1346	95	below_threshold
Leptobacterium flavescens	strain=KCTC 22160	GCA_010671605.1	472055	472055	type	True	76.8127	101	1346	95	below_threshold
Robertkochia marina	strain=CC-AMO-30D	GCA_004799345.1	1227945	1227945	type	True	76.7785	87	1346	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.7622	121	1346	95	below_threshold
Algibacter onchidii	strain=XY-114	GCA_004804355.1	2562860	2562860	type	True	76.6395	58	1346	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.6153	51	1346	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	76.5949	102	1346	95	below_threshold
Flavobacterium cerinum	strain=1E403	GCA_004028155.1	2502784	2502784	type	True	76.4862	52	1346	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	76.4815	64	1346	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	76.481	74	1346	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	76.4501	61	1346	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.2611	70	1346	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	76.1193	56	1346	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:20,890] [INFO] DFAST Taxonomy check result was written to GCF_022760175.1_ASM2276017v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:20,891] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:20,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:20,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb367178-0543-4cf1-910b-50907312b875/dqc_reference/checkm_data
[2024-01-25 17:44:20,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:20,938] [INFO] Task started: CheckM
[2024-01-25 17:44:20,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022760175.1_ASM2276017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022760175.1_ASM2276017v1_genomic.fna/checkm_input GCF_022760175.1_ASM2276017v1_genomic.fna/checkm_result
[2024-01-25 17:44:59,690] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:59,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:59,705] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:59,706] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:59,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022760175.1_ASM2276017v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:59,706] [INFO] Task started: Blastn
[2024-01-25 17:44:59,706] [INFO] Running command: blastn -query GCF_022760175.1_ASM2276017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb367178-0543-4cf1-910b-50907312b875/dqc_reference/reference_markers_gtdb.fasta -out GCF_022760175.1_ASM2276017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:00,636] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:00,640] [INFO] Selected 27 target genomes.
[2024-01-25 17:45:00,640] [INFO] Target genome list was writen to GCF_022760175.1_ASM2276017v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:00,701] [INFO] Task started: fastANI
[2024-01-25 17:45:00,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4c5d076-ecf6-4965-8164-c135be8bf545/GCF_022760175.1_ASM2276017v1_genomic.fna.gz --refList GCF_022760175.1_ASM2276017v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022760175.1_ASM2276017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:17,670] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:17,684] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:45:17,684] [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_900116365.1	s__Zhouia amylolytica	79.6811	521	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zhouia	95.0	98.62	98.62	0.95	0.95	2	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	78.4794	54	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_013402795.1	s__Costertonia aggregata	78.2149	63	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Costertonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391805.1	s__Galbibacter_A sp013391805	77.8425	100	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734785.1	s__Galbibacter_A mesophilus	77.4728	110	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260835.1	s__Imtechella halotolerans	77.1061	85	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Imtechella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300875.1	s__Galbibacter_B marinus	77.0311	86	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934685.1	s__Lacinutrix sp000934685	77.0256	62	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013365535.1	s__Aquimarina sp013365535	77.0	71	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260205.1	s__Winogradskyella tangerina	76.8378	61	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671605.1	s__Leptobacterium flavescens	76.8127	101	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799345.1	s__Robertkochia marina	76.7552	88	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014526325.1	s__Psychroserpens algicola	76.6869	54	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804355.1	s__Tamlana_C sp004804355	76.6395	58	1346	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_900116665.1	s__Pustulibacterium marinum	76.5991	103	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pustulibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028155.1	s__Flavobacterium cerinum	76.5254	51	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	76.481	74	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944795.1	s__Mangrovimonas spongiae	76.3601	61	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	76.3487	53	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	76.278	69	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299535.1	s__Aquimarina sp900299535	76.1763	68	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_004804315.1	s__Muricauda sp004804315	76.1066	55	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784145.1	s__Yeosuana sp002784145	76.0544	54	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCA_002746415.1	s__Saonia sp002746415	75.9733	56	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	75.8897	75	1346	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:17,687] [INFO] GTDB search result was written to GCF_022760175.1_ASM2276017v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:17,687] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:17,691] [INFO] DFAST_QC result json was written to GCF_022760175.1_ASM2276017v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:17,691] [INFO] DFAST_QC completed!
[2024-01-25 17:45:17,691] [INFO] Total running time: 0h1m27s