[2024-01-24 11:26:37,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:37,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:37,493] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dc93d72-9f7c-4f39-ad01-d410d9584526/dqc_reference
[2024-01-24 11:26:38,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:38,809] [INFO] Task started: Prodigal
[2024-01-24 11:26:38,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg25209d2a-461d-4713-af33-f46496be2d2c/GCF_014855515.1_ASM1485551v1_genomic.fna.gz | prodigal -d GCF_014855515.1_ASM1485551v1_genomic.fna/cds.fna -a GCF_014855515.1_ASM1485551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:59,140] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:59,141] [INFO] Task started: HMMsearch
[2024-01-24 11:26:59,141] [INFO] Running command: hmmsearch --tblout GCF_014855515.1_ASM1485551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dc93d72-9f7c-4f39-ad01-d410d9584526/dqc_reference/reference_markers.hmm GCF_014855515.1_ASM1485551v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:59,443] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:59,444] [INFO] Found 6/6 markers.
[2024-01-24 11:26:59,487] [INFO] Query marker FASTA was written to GCF_014855515.1_ASM1485551v1_genomic.fna/markers.fasta
[2024-01-24 11:26:59,487] [INFO] Task started: Blastn
[2024-01-24 11:26:59,487] [INFO] Running command: blastn -query GCF_014855515.1_ASM1485551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dc93d72-9f7c-4f39-ad01-d410d9584526/dqc_reference/reference_markers.fasta -out GCF_014855515.1_ASM1485551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:00,133] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:00,138] [INFO] Selected 26 target genomes.
[2024-01-24 11:27:00,139] [INFO] Target genome list was writen to GCF_014855515.1_ASM1485551v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:00,185] [INFO] Task started: fastANI
[2024-01-24 11:27:00,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg25209d2a-461d-4713-af33-f46496be2d2c/GCF_014855515.1_ASM1485551v1_genomic.fna.gz --refList GCF_014855515.1_ASM1485551v1_genomic.fna/target_genomes.txt --output GCF_014855515.1_ASM1485551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:17,934] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:17,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dc93d72-9f7c-4f39-ad01-d410d9584526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:17,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dc93d72-9f7c-4f39-ad01-d410d9584526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:17,951] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:17,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:17,951] [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
Euzebyella marina	strain=CY01	GCA_014855515.1	1761453	1761453	type	True	100.0	1554	1554	95	conclusive
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	79.9541	538	1554	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	79.891	117	1554	95	below_threshold
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	78.9825	50	1554	95	below_threshold
Zhouia spongiae	strain=HN-Y44	GCA_022760175.1	2202721	2202721	type	True	78.3113	61	1554	95	below_threshold
Pareuzebyella sediminis	strain=S2-4-21	GCA_008367235.1	2607998	2607998	type	True	77.4002	216	1554	95	below_threshold
Zobellia galactanivorans	strain=DsiJT	GCA_000973105.1	63186	63186	type	True	77.3278	241	1554	95	below_threshold
Zobellia uliginosa	strain=DSM 2061	GCA_900156625.1	143224	143224	type	True	77.0573	256	1554	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	77.03	240	1554	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	76.9124	141	1554	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	76.8876	171	1554	95	below_threshold
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	76.8271	144	1554	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.6879	99	1554	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	76.4063	55	1554	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	76.296	124	1554	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.2213	69	1554	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	75.7355	54	1554	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:17,953] [INFO] DFAST Taxonomy check result was written to GCF_014855515.1_ASM1485551v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:17,953] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:17,953] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:17,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dc93d72-9f7c-4f39-ad01-d410d9584526/dqc_reference/checkm_data
[2024-01-24 11:27:17,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:17,999] [INFO] Task started: CheckM
[2024-01-24 11:27:17,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014855515.1_ASM1485551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014855515.1_ASM1485551v1_genomic.fna/checkm_input GCF_014855515.1_ASM1485551v1_genomic.fna/checkm_result
[2024-01-24 11:28:16,688] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:16,690] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:16,709] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:16,709] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:16,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014855515.1_ASM1485551v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:16,710] [INFO] Task started: Blastn
[2024-01-24 11:28:16,710] [INFO] Running command: blastn -query GCF_014855515.1_ASM1485551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dc93d72-9f7c-4f39-ad01-d410d9584526/dqc_reference/reference_markers_gtdb.fasta -out GCF_014855515.1_ASM1485551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:17,547] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:17,551] [INFO] Selected 25 target genomes.
[2024-01-24 11:28:17,551] [INFO] Target genome list was writen to GCF_014855515.1_ASM1485551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:17,599] [INFO] Task started: fastANI
[2024-01-24 11:28:17,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg25209d2a-461d-4713-af33-f46496be2d2c/GCF_014855515.1_ASM1485551v1_genomic.fna.gz --refList GCF_014855515.1_ASM1485551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014855515.1_ASM1485551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:34,908] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:34,929] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:34,929] [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_014855515.1	s__Euzebyella marina	100.0	1554	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	97.49	97.10	0.92	0.88	10	conclusive
GCF_014349235.1	s__Euzebyella sp014349235	82.1501	563	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014855495.1	s__Euzebyella saccharophila	79.9546	538	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382275.1	s__Muricauda nanhaiensis	79.8457	118	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017810075.1	s__Pseudozobellia sp017810075	78.7064	473	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813285.1	s__Pseudozobellia sp002813285	78.1286	458	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141855.1	s__Pseudozobellia thermophila	77.9206	311	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973105.1	s__Zobellia galactanivorans	77.3278	241	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
GCA_011050085.1	s__Pricia antarctica_A	77.0612	170	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pricia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156625.1	s__Zobellia uliginosa	77.0573	256	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232155.1	s__RZ26 sp003232155	77.0309	87	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142175.1	s__Maribacter aquivivus	76.9301	140	1554	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	76.9014	170	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_009649685.1	s__Aurantibacter_A sp009649685	76.8092	124	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001935.1	s__Maribacter_A sp013001935	76.5447	63	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	96.76	96.72	0.66	0.66	3	-
GCF_009184425.1	s__Muricauda olearia	76.3256	106	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_000733925.1	s__Arenibacter algicola	76.3115	123	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_002514735.1	s__Sediminicola_A luteus	76.2586	88	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sediminicola_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:34,931] [INFO] GTDB search result was written to GCF_014855515.1_ASM1485551v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:34,931] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:34,935] [INFO] DFAST_QC result json was written to GCF_014855515.1_ASM1485551v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:34,935] [INFO] DFAST_QC completed!
[2024-01-24 11:28:34,936] [INFO] Total running time: 0h1m57s