[2024-01-25 18:13:51,106] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:51,107] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:51,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ff365e8-65fe-49ce-ba70-d988797f9a84/dqc_reference
[2024-01-25 18:13:52,250] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:52,251] [INFO] Task started: Prodigal
[2024-01-25 18:13:52,251] [INFO] Running command: gunzip -c /var/lib/cwl/stgacf6d563-0d11-48e6-8987-24436f38979b/GCF_023721415.1_ASM2372141v1_genomic.fna.gz | prodigal -d GCF_023721415.1_ASM2372141v1_genomic.fna/cds.fna -a GCF_023721415.1_ASM2372141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:05,121] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:05,122] [INFO] Task started: HMMsearch
[2024-01-25 18:14:05,122] [INFO] Running command: hmmsearch --tblout GCF_023721415.1_ASM2372141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ff365e8-65fe-49ce-ba70-d988797f9a84/dqc_reference/reference_markers.hmm GCF_023721415.1_ASM2372141v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:05,396] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:05,397] [INFO] Found 6/6 markers.
[2024-01-25 18:14:05,434] [INFO] Query marker FASTA was written to GCF_023721415.1_ASM2372141v1_genomic.fna/markers.fasta
[2024-01-25 18:14:05,434] [INFO] Task started: Blastn
[2024-01-25 18:14:05,434] [INFO] Running command: blastn -query GCF_023721415.1_ASM2372141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ff365e8-65fe-49ce-ba70-d988797f9a84/dqc_reference/reference_markers.fasta -out GCF_023721415.1_ASM2372141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:06,104] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:06,113] [INFO] Selected 25 target genomes.
[2024-01-25 18:14:06,114] [INFO] Target genome list was writen to GCF_023721415.1_ASM2372141v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:06,149] [INFO] Task started: fastANI
[2024-01-25 18:14:06,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgacf6d563-0d11-48e6-8987-24436f38979b/GCF_023721415.1_ASM2372141v1_genomic.fna.gz --refList GCF_023721415.1_ASM2372141v1_genomic.fna/target_genomes.txt --output GCF_023721415.1_ASM2372141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:20,786] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:20,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ff365e8-65fe-49ce-ba70-d988797f9a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:20,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ff365e8-65fe-49ce-ba70-d988797f9a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:20,802] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:14:20,802] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:14:20,802] [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
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	79.1084	434	1253	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	78.7441	397	1253	95	below_threshold
Galbibacter marinus	strain=ck-I2-15	GCA_000300875.1	555500	555500	type	True	78.118	155	1253	95	below_threshold
Robertkochia solimangrovi	strain=CL23	GCA_007279655.1	2213046	2213046	type	True	77.1953	118	1253	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.1636	72	1253	95	below_threshold
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	76.9451	79	1253	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	76.8937	112	1253	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.876	92	1253	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.7035	87	1253	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	76.695	86	1253	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.695	86	1253	95	below_threshold
Tamlana crocina	strain=HST1-43	GCA_012037625.1	393006	393006	type	True	76.657	93	1253	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.6406	80	1253	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	76.6359	91	1253	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	76.6163	67	1253	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	76.5601	88	1253	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.5472	75	1253	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.4506	90	1253	95	below_threshold
Salegentibacter maritimus	strain=F63223	GCA_016236915.1	2794347	2794347	type	True	76.4316	98	1253	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.4139	89	1253	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	76.3998	67	1253	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.3486	96	1253	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.3358	72	1253	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.2635	95	1253	95	below_threshold
Flavobacterium urocaniciphilum	strain=DSM 27078	GCA_900110615.1	1299341	1299341	type	True	76.1498	58	1253	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:20,804] [INFO] DFAST Taxonomy check result was written to GCF_023721415.1_ASM2372141v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:20,804] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:20,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:20,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ff365e8-65fe-49ce-ba70-d988797f9a84/dqc_reference/checkm_data
[2024-01-25 18:14:20,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:20,848] [INFO] Task started: CheckM
[2024-01-25 18:14:20,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023721415.1_ASM2372141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023721415.1_ASM2372141v1_genomic.fna/checkm_input GCF_023721415.1_ASM2372141v1_genomic.fna/checkm_result
[2024-01-25 18:14:58,890] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:58,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:58,914] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:58,914] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:58,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023721415.1_ASM2372141v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:58,914] [INFO] Task started: Blastn
[2024-01-25 18:14:58,914] [INFO] Running command: blastn -query GCF_023721415.1_ASM2372141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ff365e8-65fe-49ce-ba70-d988797f9a84/dqc_reference/reference_markers_gtdb.fasta -out GCF_023721415.1_ASM2372141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:59,807] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:59,810] [INFO] Selected 20 target genomes.
[2024-01-25 18:14:59,810] [INFO] Target genome list was writen to GCF_023721415.1_ASM2372141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:59,822] [INFO] Task started: fastANI
[2024-01-25 18:14:59,823] [INFO] Running command: fastANI --query /var/lib/cwl/stgacf6d563-0d11-48e6-8987-24436f38979b/GCF_023721415.1_ASM2372141v1_genomic.fna.gz --refList GCF_023721415.1_ASM2372141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023721415.1_ASM2372141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:12,806] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:12,820] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:12,820] [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_016734785.1	s__Galbibacter_A mesophilus	99.9959	1249	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013391805.1	s__Galbibacter_A sp013391805	81.2276	639	1253	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_000260115.1	s__Joostella marina	79.115	432	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Joostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300875.1	s__Galbibacter_B marinus	78.118	155	1253	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_007279655.1	s__Robertkochia solimangrovi	77.1953	118	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116665.1	s__Pustulibacterium marinum	76.8889	111	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pustulibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215465.1	s__Muricauda pacifica_A	76.7103	63	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	76.695	86	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCA_001874145.1	s__Lacinutrix sp001874145	76.6829	80	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115185.1	s__Algorimicrobium echini	76.5599	75	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	97.77	97.77	0.81	0.81	2	-
GCA_016744625.1	s__Winogradskyella sp016744625	76.5596	63	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685485.1	s__Formosa haliotis	76.5581	94	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	76.4389	96	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_016236915.1	s__Salegentibacter maritimus	76.4316	98	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	98.25	98.21	0.91	0.91	3	-
GCF_900102055.1	s__Ulvibacter litoralis	76.4116	88	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000797445.1	s__Lacinutrix jangbogonensis	76.3842	66	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757735.1	s__Aequorivita sp016757735	76.3165	73	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102165.1	s__Cellulophaga baltica	76.2597	94	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_008040165.1	s__Muricauda hymeniacidonis	76.2301	76	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	75.8819	90	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:12,822] [INFO] GTDB search result was written to GCF_023721415.1_ASM2372141v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:12,822] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:12,826] [INFO] DFAST_QC result json was written to GCF_023721415.1_ASM2372141v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:12,826] [INFO] DFAST_QC completed!
[2024-01-25 18:15:12,826] [INFO] Total running time: 0h1m22s