[2024-01-24 12:52:26,684] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:26,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:26,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f0d39e1-c00d-4aca-b974-0caddb8c3633/dqc_reference
[2024-01-24 12:52:27,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:27,930] [INFO] Task started: Prodigal
[2024-01-24 12:52:27,930] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5071728-96b8-470f-bf7a-2f35d8a25c6f/GCF_004362865.1_ASM436286v1_genomic.fna.gz | prodigal -d GCF_004362865.1_ASM436286v1_genomic.fna/cds.fna -a GCF_004362865.1_ASM436286v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:43,056] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:43,057] [INFO] Task started: HMMsearch
[2024-01-24 12:52:43,057] [INFO] Running command: hmmsearch --tblout GCF_004362865.1_ASM436286v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f0d39e1-c00d-4aca-b974-0caddb8c3633/dqc_reference/reference_markers.hmm GCF_004362865.1_ASM436286v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:43,380] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:43,381] [INFO] Found 6/6 markers.
[2024-01-24 12:52:43,416] [INFO] Query marker FASTA was written to GCF_004362865.1_ASM436286v1_genomic.fna/markers.fasta
[2024-01-24 12:52:43,417] [INFO] Task started: Blastn
[2024-01-24 12:52:43,417] [INFO] Running command: blastn -query GCF_004362865.1_ASM436286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f0d39e1-c00d-4aca-b974-0caddb8c3633/dqc_reference/reference_markers.fasta -out GCF_004362865.1_ASM436286v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:44,084] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:44,090] [INFO] Selected 27 target genomes.
[2024-01-24 12:52:44,090] [INFO] Target genome list was writen to GCF_004362865.1_ASM436286v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:44,121] [INFO] Task started: fastANI
[2024-01-24 12:52:44,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5071728-96b8-470f-bf7a-2f35d8a25c6f/GCF_004362865.1_ASM436286v1_genomic.fna.gz --refList GCF_004362865.1_ASM436286v1_genomic.fna/target_genomes.txt --output GCF_004362865.1_ASM436286v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:02,117] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:02,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f0d39e1-c00d-4aca-b974-0caddb8c3633/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:02,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f0d39e1-c00d-4aca-b974-0caddb8c3633/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:02,142] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:53:02,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:02,142] [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
Zeaxanthinibacter enoshimensis	strain=DSM 18435	GCA_004362865.1	392009	392009	type	True	100.0	1106	1106	95	conclusive
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	78.178	72	1106	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	77.6215	62	1106	95	below_threshold
Euzebyella marina	strain=CY01	GCA_014855515.1	1761453	1761453	type	True	77.3294	67	1106	95	below_threshold
Arenibacter aquaticus	strain=GUO	GCA_003957295.1	2489054	2489054	type	True	77.1051	86	1106	95	below_threshold
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	77.0509	136	1106	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	76.9486	74	1106	95	below_threshold
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	76.8837	57	1106	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	76.8675	75	1106	95	below_threshold
Muriicola jejuensis	strain=KCTC 22299	GCA_010671595.1	504488	504488	type	True	76.815	137	1106	95	below_threshold
Muriicola soli	strain=MMS17-SY002	GCA_004139715.1	2507538	2507538	type	True	76.7979	95	1106	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	76.7961	55	1106	95	below_threshold
Robertkochia marina	strain=CC-AMO-30D	GCA_007279605.1	1227945	1227945	type	True	76.6943	62	1106	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	76.6899	73	1106	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	76.6591	74	1106	95	below_threshold
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.6111	67	1106	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	76.597	74	1106	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.5445	94	1106	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.5415	122	1106	95	below_threshold
Robiginitalea sediminis	strain=O458	GCA_002198115.1	1982593	1982593	type	True	76.527	96	1106	95	below_threshold
Robertkochia marina	strain=CC-AMO-30D	GCA_004799345.1	1227945	1227945	type	True	76.455	61	1106	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:02,144] [INFO] DFAST Taxonomy check result was written to GCF_004362865.1_ASM436286v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:02,145] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:02,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:02,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f0d39e1-c00d-4aca-b974-0caddb8c3633/dqc_reference/checkm_data
[2024-01-24 12:53:02,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:02,188] [INFO] Task started: CheckM
[2024-01-24 12:53:02,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362865.1_ASM436286v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362865.1_ASM436286v1_genomic.fna/checkm_input GCF_004362865.1_ASM436286v1_genomic.fna/checkm_result
[2024-01-24 12:53:46,691] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:46,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:46,718] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:46,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:46,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362865.1_ASM436286v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:46,719] [INFO] Task started: Blastn
[2024-01-24 12:53:46,720] [INFO] Running command: blastn -query GCF_004362865.1_ASM436286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f0d39e1-c00d-4aca-b974-0caddb8c3633/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362865.1_ASM436286v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:47,547] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:47,551] [INFO] Selected 21 target genomes.
[2024-01-24 12:53:47,551] [INFO] Target genome list was writen to GCF_004362865.1_ASM436286v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:47,591] [INFO] Task started: fastANI
[2024-01-24 12:53:47,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5071728-96b8-470f-bf7a-2f35d8a25c6f/GCF_004362865.1_ASM436286v1_genomic.fna.gz --refList GCF_004362865.1_ASM436286v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362865.1_ASM436286v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:01,382] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:01,398] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:01,399] [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_004362865.1	s__Zeaxanthinibacter enoshimensis	100.0	1106	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013003145.1	s__Zeaxanthinibacter sp013003145	82.4214	455	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014855515.1	s__Euzebyella marina	77.3302	67	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	97.49	97.10	0.92	0.88	10	-
GCF_002742265.1	s__Maribacter sp002742265	77.2341	62	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957295.1	s__Arenibacter aquaticus	77.1051	86	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	77.0857	85	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_014638095.1	s__Muriicola marianensis	77.0509	136	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001683915.1	s__Muricauda sp001683915	76.9716	79	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCA_001683825.1	s__Zeaxanthinibacter sp001683825	76.8554	180	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011068285.1	s__Muricauda sp011068285	76.8352	76	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671595.1	s__Muriicola jejuensis	76.815	137	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003285545.1	s__Sinomicrobium sp003285545	76.7586	54	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699205.1	s__Muricauda sp002699205	76.6574	71	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
GCA_009371985.2	s__TP-CH-4 sp009371985	76.6111	67	1106	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_002198115.1	s__Robiginitalea sediminis	76.527	96	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009901585.1	s__R33 sp009901585	76.5246	123	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__R33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058265.1	s__Muricauda sp003058265	76.522	95	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799345.1	s__Robertkochia marina	76.455	61	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003201775.1	s__Arenibacter sp003201775	76.1902	83	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:01,401] [INFO] GTDB search result was written to GCF_004362865.1_ASM436286v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:01,402] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:01,410] [INFO] DFAST_QC result json was written to GCF_004362865.1_ASM436286v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:01,411] [INFO] DFAST_QC completed!
[2024-01-24 12:54:01,411] [INFO] Total running time: 0h1m35s