[2024-01-24 11:48:21,284] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,287] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg195a194e-65e3-44d1-aefc-bae4e0e7d74a/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,566] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,566] [INFO] Running command: gunzip -c /var/lib/cwl/stg68aa0965-4f03-4c96-bca7-2e27947024b5/GCF_011927795.1_ASM1192779v1_genomic.fna.gz | prodigal -d GCF_011927795.1_ASM1192779v1_genomic.fna/cds.fna -a GCF_011927795.1_ASM1192779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:41,582] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:41,583] [INFO] Task started: HMMsearch
[2024-01-24 11:48:41,583] [INFO] Running command: hmmsearch --tblout GCF_011927795.1_ASM1192779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg195a194e-65e3-44d1-aefc-bae4e0e7d74a/dqc_reference/reference_markers.hmm GCF_011927795.1_ASM1192779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:41,854] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:41,856] [INFO] Found 6/6 markers.
[2024-01-24 11:48:41,889] [INFO] Query marker FASTA was written to GCF_011927795.1_ASM1192779v1_genomic.fna/markers.fasta
[2024-01-24 11:48:41,890] [INFO] Task started: Blastn
[2024-01-24 11:48:41,890] [INFO] Running command: blastn -query GCF_011927795.1_ASM1192779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg195a194e-65e3-44d1-aefc-bae4e0e7d74a/dqc_reference/reference_markers.fasta -out GCF_011927795.1_ASM1192779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:42,593] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:42,598] [INFO] Selected 30 target genomes.
[2024-01-24 11:48:42,598] [INFO] Target genome list was writen to GCF_011927795.1_ASM1192779v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:42,610] [INFO] Task started: fastANI
[2024-01-24 11:48:42,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg68aa0965-4f03-4c96-bca7-2e27947024b5/GCF_011927795.1_ASM1192779v1_genomic.fna.gz --refList GCF_011927795.1_ASM1192779v1_genomic.fna/target_genomes.txt --output GCF_011927795.1_ASM1192779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:49:02,340] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:02,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg195a194e-65e3-44d1-aefc-bae4e0e7d74a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:49:02,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg195a194e-65e3-44d1-aefc-bae4e0e7d74a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:49:02,368] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:49:02,368] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:49:02,369] [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
Saonia flava	strain=DSM 29762	GCA_011927795.1	523696	523696	type	True	100.0	1264	1264	95	conclusive
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	77.0357	164	1264	95	below_threshold
Costertonia aggregata	strain=KCCM 42265	GCA_013402795.1	343403	343403	type	True	76.9702	175	1264	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	76.9492	179	1264	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	76.9488	179	1264	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.9252	215	1264	95	below_threshold
Muriicola soli	strain=MMS17-SY002	GCA_004139715.1	2507538	2507538	type	True	76.9246	70	1264	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.8921	166	1264	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.8683	186	1264	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	76.8168	169	1264	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	76.8047	207	1264	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	76.7948	193	1264	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.7938	186	1264	95	below_threshold
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	76.7725	136	1264	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.7387	185	1264	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	76.7321	188	1264	95	below_threshold
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	76.7315	177	1264	95	below_threshold
Croceitalea dokdonensis	strain=DOKDO 023	GCA_001306415.1	346188	346188	type	True	76.6937	131	1264	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.653	86	1264	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	76.6234	124	1264	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.5729	89	1264	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.5538	147	1264	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	76.5329	102	1264	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	76.5234	188	1264	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.3761	83	1264	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	76.3474	70	1264	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	76.3302	59	1264	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.2146	93	1264	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.1752	91	1264	95	below_threshold
Kordia aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	76.1296	79	1264	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:49:02,371] [INFO] DFAST Taxonomy check result was written to GCF_011927795.1_ASM1192779v1_genomic.fna/tc_result.tsv
[2024-01-24 11:49:02,371] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:49:02,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:49:02,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg195a194e-65e3-44d1-aefc-bae4e0e7d74a/dqc_reference/checkm_data
[2024-01-24 11:49:02,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:49:02,412] [INFO] Task started: CheckM
[2024-01-24 11:49:02,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011927795.1_ASM1192779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011927795.1_ASM1192779v1_genomic.fna/checkm_input GCF_011927795.1_ASM1192779v1_genomic.fna/checkm_result
[2024-01-24 11:49:51,072] [INFO] Task succeeded: CheckM
[2024-01-24 11:49:51,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:49:51,091] [INFO] ===== Completeness check finished =====
[2024-01-24 11:49:51,091] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:49:51,092] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011927795.1_ASM1192779v1_genomic.fna/markers.fasta)
[2024-01-24 11:49:51,092] [INFO] Task started: Blastn
[2024-01-24 11:49:51,092] [INFO] Running command: blastn -query GCF_011927795.1_ASM1192779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg195a194e-65e3-44d1-aefc-bae4e0e7d74a/dqc_reference/reference_markers_gtdb.fasta -out GCF_011927795.1_ASM1192779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:49:52,019] [INFO] Task succeeded: Blastn
[2024-01-24 11:49:52,024] [INFO] Selected 26 target genomes.
[2024-01-24 11:49:52,024] [INFO] Target genome list was writen to GCF_011927795.1_ASM1192779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:49:52,043] [INFO] Task started: fastANI
[2024-01-24 11:49:52,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg68aa0965-4f03-4c96-bca7-2e27947024b5/GCF_011927795.1_ASM1192779v1_genomic.fna.gz --refList GCF_011927795.1_ASM1192779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011927795.1_ASM1192779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:50:11,278] [INFO] Task succeeded: fastANI
[2024-01-24 11:50:11,303] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:50:11,303] [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_011927795.1	s__Saonia flava	100.0	1264	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002746415.1	s__Saonia sp002746415	78.1765	432	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596745.1	s__Maribacter_A sp014596745	77.0763	154	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232155.1	s__RZ26 sp003232155	77.0632	101	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272855.1	s__Arenibacter sp012272855	77.0104	138	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013402795.1	s__Costertonia aggregata	76.9702	175	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Costertonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397245.1	s__Arenibacter arenosicollis	76.9488	179	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004139715.1	s__Muriicola sp004139715	76.9246	70	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634105.1	s__Maribacter_B vaceletii	76.9166	216	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	76.8889	187	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	76.8798	185	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993815.1	s__Muricauda sp010993815	76.8464	158	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009797025.1	s__Cellulophaga sp009797025	76.8419	176	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	76.8268	197	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860745.1	s__Zobellia uliginosa_B	76.7895	173	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014610845.1	s__Maribacter_A arenosus	76.7578	137	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215465.1	s__Muricauda pacifica_A	76.7408	186	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861125.1	s__Cellulophaga baltica_A	76.6975	185	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449435.1	s__Muricauda sp018449435	76.6463	168	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	76.5876	145	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349235.1	s__Euzebyella sp014349235	76.5711	166	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	76.5407	165	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	76.5034	133	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167435.2	s__Muricauda sp002167435	76.477	139	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224335.1	s__Algorimicrobium argentinense	76.3683	59	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	76.1339	97	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:50:11,305] [INFO] GTDB search result was written to GCF_011927795.1_ASM1192779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:50:11,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:50:11,310] [INFO] DFAST_QC result json was written to GCF_011927795.1_ASM1192779v1_genomic.fna/dqc_result.json
[2024-01-24 11:50:11,310] [INFO] DFAST_QC completed!
[2024-01-24 11:50:11,310] [INFO] Total running time: 0h1m50s