[2024-01-24 14:21:49,151] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:49,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:49,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d4b28b1-738b-43a0-8996-d794b709cd00/dqc_reference
[2024-01-24 14:21:50,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:50,445] [INFO] Task started: Prodigal
[2024-01-24 14:21:50,445] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e937a94-68e3-4b91-b3e6-dd49568fa35f/GCF_005943945.1_ASM594394v1_genomic.fna.gz | prodigal -d GCF_005943945.1_ASM594394v1_genomic.fna/cds.fna -a GCF_005943945.1_ASM594394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:13,977] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:13,978] [INFO] Task started: HMMsearch
[2024-01-24 14:22:13,978] [INFO] Running command: hmmsearch --tblout GCF_005943945.1_ASM594394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d4b28b1-738b-43a0-8996-d794b709cd00/dqc_reference/reference_markers.hmm GCF_005943945.1_ASM594394v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:14,283] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:14,285] [INFO] Found 6/6 markers.
[2024-01-24 14:22:14,328] [INFO] Query marker FASTA was written to GCF_005943945.1_ASM594394v1_genomic.fna/markers.fasta
[2024-01-24 14:22:14,328] [INFO] Task started: Blastn
[2024-01-24 14:22:14,328] [INFO] Running command: blastn -query GCF_005943945.1_ASM594394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d4b28b1-738b-43a0-8996-d794b709cd00/dqc_reference/reference_markers.fasta -out GCF_005943945.1_ASM594394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:15,007] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:15,010] [INFO] Selected 26 target genomes.
[2024-01-24 14:22:15,011] [INFO] Target genome list was writen to GCF_005943945.1_ASM594394v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:15,022] [INFO] Task started: fastANI
[2024-01-24 14:22:15,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e937a94-68e3-4b91-b3e6-dd49568fa35f/GCF_005943945.1_ASM594394v1_genomic.fna.gz --refList GCF_005943945.1_ASM594394v1_genomic.fna/target_genomes.txt --output GCF_005943945.1_ASM594394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:33,107] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:33,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d4b28b1-738b-43a0-8996-d794b709cd00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:33,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d4b28b1-738b-43a0-8996-d794b709cd00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:33,126] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:33,126] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:33,127] [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
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	100.0	1574	1574	95	conclusive
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.9741	208	1574	95	below_threshold
Croceitalea dokdonensis	strain=DOKDO 023	GCA_001306415.1	346188	346188	type	True	76.8978	92	1574	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	76.8879	115	1574	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	76.8631	105	1574	95	below_threshold
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	76.8418	86	1574	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	76.7793	98	1574	95	below_threshold
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	76.694	140	1574	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	76.6529	90	1574	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	76.6529	90	1574	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.6275	144	1574	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.6174	196	1574	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	76.6128	64	1574	95	below_threshold
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	76.4841	138	1574	95	below_threshold
Zobellia uliginosa	strain=DSM 2061	GCA_900156625.1	143224	143224	type	True	76.4653	159	1574	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	76.4146	139	1574	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	76.3729	82	1574	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	76.3428	95	1574	95	below_threshold
Arenibacter hampyeongensis	strain=JCM 17788	GCA_002909255.1	1028743	1028743	type	True	76.2966	106	1574	95	below_threshold
Muricauda ochracea	strain=JGD-17	GCA_009903685.1	2696472	2696472	type	True	76.2863	75	1574	95	below_threshold
Pricia antarctica	strain=DSM 23421	GCA_900101815.1	641691	641691	type	True	76.1729	157	1574	95	below_threshold
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	76.0972	88	1574	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:33,128] [INFO] DFAST Taxonomy check result was written to GCF_005943945.1_ASM594394v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:33,129] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:33,129] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:33,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d4b28b1-738b-43a0-8996-d794b709cd00/dqc_reference/checkm_data
[2024-01-24 14:22:33,131] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:33,182] [INFO] Task started: CheckM
[2024-01-24 14:22:33,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005943945.1_ASM594394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005943945.1_ASM594394v1_genomic.fna/checkm_input GCF_005943945.1_ASM594394v1_genomic.fna/checkm_result
[2024-01-24 14:23:37,855] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:37,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:37,879] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:37,879] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:37,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005943945.1_ASM594394v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:37,880] [INFO] Task started: Blastn
[2024-01-24 14:23:37,880] [INFO] Running command: blastn -query GCF_005943945.1_ASM594394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d4b28b1-738b-43a0-8996-d794b709cd00/dqc_reference/reference_markers_gtdb.fasta -out GCF_005943945.1_ASM594394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:38,789] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:38,794] [INFO] Selected 26 target genomes.
[2024-01-24 14:23:38,795] [INFO] Target genome list was writen to GCF_005943945.1_ASM594394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:38,813] [INFO] Task started: fastANI
[2024-01-24 14:23:38,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e937a94-68e3-4b91-b3e6-dd49568fa35f/GCF_005943945.1_ASM594394v1_genomic.fna.gz --refList GCF_005943945.1_ASM594394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005943945.1_ASM594394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:01,652] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:01,677] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:01,678] [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
GCA_005943945.1	s__F202Z8 sp005943945	100.0	1574	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__F202Z8	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009371985.2	s__TP-CH-4 sp009371985	76.9628	208	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TP-CH-4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306415.1	s__Croceitalea dokdonensis	76.8908	90	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015330165.1	s__Zobellia sp015330165	76.8879	115	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.41	98.41	0.92	0.92	2	-
GCF_014855495.1	s__Euzebyella saccharophila	76.8418	86	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	76.8251	67	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003232435.1	s__Aurantibacter_A sp003232435	76.8045	110	1574	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_900109345.1	s__Maribacter orientalis	76.7793	98	1574	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	76.7279	103	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269385.1	s__Maribacter cobaltidurans	76.7136	141	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	76.6364	144	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCF_005885635.1	s__RZ26 sp005885635	76.6177	197	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057865.1	s__Muricauda brasiliensis	76.6128	64	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_003626755.1	s__Ulvibacterium marinum	76.4843	130	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156625.1	s__Zobellia uliginosa	76.4653	159	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584135.1	s__Muricauda sp003584135	76.4646	89	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003232155.1	s__RZ26 sp003232155	76.4578	89	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149745.1	s__Muricauda koreensis	76.3465	89	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449435.1	s__Muricauda sp018449435	76.3431	93	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050085.1	s__Pricia antarctica_A	76.3167	119	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pricia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909255.1	s__Arenibacter hampyeongensis	76.2966	106	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101815.1	s__Pricia antarctica	76.1825	156	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pricia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479535.1	s__Maribacter sp905479535	76.1049	76	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500845.1	s__Muricauda sediminis	76.0972	88	1574	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:01,680] [INFO] GTDB search result was written to GCF_005943945.1_ASM594394v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:01,681] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:01,686] [INFO] DFAST_QC result json was written to GCF_005943945.1_ASM594394v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:01,686] [INFO] DFAST_QC completed!
[2024-01-24 14:24:01,686] [INFO] Total running time: 0h2m13s