[2024-01-24 13:46:01,646] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,649] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,649] [INFO] DQC Reference Directory: /var/lib/cwl/stg77ac3da0-4893-4181-bd55-4450140e9b9c/dqc_reference
[2024-01-24 13:46:02,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,991] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,992] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1a8fe82-9146-41ee-aa8d-179b1d71a418/GCF_000621125.1_ASM62112v1_genomic.fna.gz | prodigal -d GCF_000621125.1_ASM62112v1_genomic.fna/cds.fna -a GCF_000621125.1_ASM62112v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:22,304] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:22,305] [INFO] Task started: HMMsearch
[2024-01-24 13:46:22,305] [INFO] Running command: hmmsearch --tblout GCF_000621125.1_ASM62112v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77ac3da0-4893-4181-bd55-4450140e9b9c/dqc_reference/reference_markers.hmm GCF_000621125.1_ASM62112v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:22,619] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:22,620] [INFO] Found 6/6 markers.
[2024-01-24 13:46:22,675] [INFO] Query marker FASTA was written to GCF_000621125.1_ASM62112v1_genomic.fna/markers.fasta
[2024-01-24 13:46:22,676] [INFO] Task started: Blastn
[2024-01-24 13:46:22,676] [INFO] Running command: blastn -query GCF_000621125.1_ASM62112v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77ac3da0-4893-4181-bd55-4450140e9b9c/dqc_reference/reference_markers.fasta -out GCF_000621125.1_ASM62112v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:23,388] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:23,391] [INFO] Selected 24 target genomes.
[2024-01-24 13:46:23,392] [INFO] Target genome list was writen to GCF_000621125.1_ASM62112v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:23,407] [INFO] Task started: fastANI
[2024-01-24 13:46:23,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1a8fe82-9146-41ee-aa8d-179b1d71a418/GCF_000621125.1_ASM62112v1_genomic.fna.gz --refList GCF_000621125.1_ASM62112v1_genomic.fna/target_genomes.txt --output GCF_000621125.1_ASM62112v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:42,897] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:42,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77ac3da0-4893-4181-bd55-4450140e9b9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:42,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77ac3da0-4893-4181-bd55-4450140e9b9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:42,916] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:42,917] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:42,917] [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
Maribacter antarcticus	strain=DSM 21422	GCA_000621125.1	505250	505250	type	True	100.0	1601	1602	95	conclusive
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	77.3997	228	1602	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	77.3717	234	1602	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	77.319	221	1602	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	77.3079	236	1602	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	77.2006	247	1602	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	77.1133	241	1602	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	77.0731	234	1602	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	77.0672	234	1602	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	77.031	204	1602	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	76.9981	230	1602	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.9935	150	1602	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.9688	165	1602	95	below_threshold
Costertonia aggregata	strain=KCCM 42265	GCA_013402795.1	343403	343403	type	True	76.9565	171	1602	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.6531	126	1602	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	76.5471	65	1602	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	76.4906	100	1602	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.4422	157	1602	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.1734	64	1602	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.1033	76	1602	95	below_threshold
Muricauda ochracea	strain=JGD-17	GCA_009903685.1	2696472	2696472	type	True	75.9864	78	1602	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	75.9495	72	1602	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:42,919] [INFO] DFAST Taxonomy check result was written to GCF_000621125.1_ASM62112v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:42,920] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:42,920] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:42,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77ac3da0-4893-4181-bd55-4450140e9b9c/dqc_reference/checkm_data
[2024-01-24 13:46:42,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:42,970] [INFO] Task started: CheckM
[2024-01-24 13:46:42,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621125.1_ASM62112v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621125.1_ASM62112v1_genomic.fna/checkm_input GCF_000621125.1_ASM62112v1_genomic.fna/checkm_result
[2024-01-24 13:47:36,294] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:36,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:36,317] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:36,330] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:36,331] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621125.1_ASM62112v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:36,331] [INFO] Task started: Blastn
[2024-01-24 13:47:36,332] [INFO] Running command: blastn -query GCF_000621125.1_ASM62112v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77ac3da0-4893-4181-bd55-4450140e9b9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621125.1_ASM62112v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:37,146] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:37,151] [INFO] Selected 23 target genomes.
[2024-01-24 13:47:37,151] [INFO] Target genome list was writen to GCF_000621125.1_ASM62112v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:37,168] [INFO] Task started: fastANI
[2024-01-24 13:47:37,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1a8fe82-9146-41ee-aa8d-179b1d71a418/GCF_000621125.1_ASM62112v1_genomic.fna.gz --refList GCF_000621125.1_ASM62112v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621125.1_ASM62112v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:52,954] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:52,974] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:52,974] [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_000621125.1	s__Maribacter antarcticus	100.0	1601	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003970695.1	s__Maribacter sp002742365	77.5169	253	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.61	96.61	0.86	0.86	2	-
GCF_001447995.1	s__Maribacter dokdonensis	77.459	236	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_900109345.1	s__Maribacter orientalis	77.4154	229	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	77.3738	237	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	77.3199	220	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_001913155.1	s__Maribacter hydrothermalis	77.2502	248	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016811105.1	s__Aurantibacter_A crassamenti	77.1832	142	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142175.1	s__Maribacter aquivivus	77.1237	240	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001020565.1	s__Maribacter thermophilus	77.0888	206	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	77.0731	234	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100785.1	s__Maribacter sp018100785	77.0511	217	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009797025.1	s__Cellulophaga sp009797025	77.0242	151	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	77.0036	242	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004364175.1	s__Maribacter caenipelagi	76.9981	230	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190595.1	s__Cellulophaga lytica	76.8753	138	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCF_003581615.1	s__Muricauda lutimaris	76.4989	101	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009901525.1	s__Kordia antarctica	76.4868	67	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	76.4422	157	1602	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	76.228	102	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009903685.1	s__Muricauda ochracea	75.9523	80	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	75.5361	56	1602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:52,977] [INFO] GTDB search result was written to GCF_000621125.1_ASM62112v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:52,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:52,982] [INFO] DFAST_QC result json was written to GCF_000621125.1_ASM62112v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:52,983] [INFO] DFAST_QC completed!
[2024-01-24 13:47:52,983] [INFO] Total running time: 0h1m51s