[2024-01-24 13:22:41,021] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:41,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:41,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a841599-fe23-4991-826a-d614ccc66216/dqc_reference
[2024-01-24 13:22:42,496] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:42,497] [INFO] Task started: Prodigal
[2024-01-24 13:22:42,497] [INFO] Running command: gunzip -c /var/lib/cwl/stg6642e280-f37a-4567-99d2-d1e8e254cc81/GCF_015209595.1_ASM1520959v1_genomic.fna.gz | prodigal -d GCF_015209595.1_ASM1520959v1_genomic.fna/cds.fna -a GCF_015209595.1_ASM1520959v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:55,624] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:55,625] [INFO] Task started: HMMsearch
[2024-01-24 13:22:55,625] [INFO] Running command: hmmsearch --tblout GCF_015209595.1_ASM1520959v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a841599-fe23-4991-826a-d614ccc66216/dqc_reference/reference_markers.hmm GCF_015209595.1_ASM1520959v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:55,893] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:55,895] [INFO] Found 6/6 markers.
[2024-01-24 13:22:55,940] [INFO] Query marker FASTA was written to GCF_015209595.1_ASM1520959v1_genomic.fna/markers.fasta
[2024-01-24 13:22:55,941] [INFO] Task started: Blastn
[2024-01-24 13:22:55,941] [INFO] Running command: blastn -query GCF_015209595.1_ASM1520959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a841599-fe23-4991-826a-d614ccc66216/dqc_reference/reference_markers.fasta -out GCF_015209595.1_ASM1520959v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:56,632] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:56,636] [INFO] Selected 30 target genomes.
[2024-01-24 13:22:56,636] [INFO] Target genome list was writen to GCF_015209595.1_ASM1520959v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:56,651] [INFO] Task started: fastANI
[2024-01-24 13:22:56,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg6642e280-f37a-4567-99d2-d1e8e254cc81/GCF_015209595.1_ASM1520959v1_genomic.fna.gz --refList GCF_015209595.1_ASM1520959v1_genomic.fna/target_genomes.txt --output GCF_015209595.1_ASM1520959v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:15,904] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:15,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a841599-fe23-4991-826a-d614ccc66216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:15,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a841599-fe23-4991-826a-d614ccc66216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:15,921] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:23:15,921] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:23:15,921] [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
Neptuniibacter caesariensis	strain=MED92	GCA_000153345.1	207954	207954	type	True	78.7246	193	1525	95	below_threshold
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	78.3143	218	1525	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	78.2642	184	1525	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	78.2531	281	1525	95	below_threshold
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	78.2348	219	1525	95	below_threshold
Neptuniibacter marinus	strain=ATR 1.1	GCA_001597725.1	1806670	1806670	type	True	78.2217	91	1525	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	77.9899	152	1525	95	below_threshold
Neptuniibacter pectenicola	strain=LFT 1.8	GCA_001597735.1	1806669	1806669	type	True	77.6167	126	1525	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	77.602	132	1525	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	77.4054	147	1525	95	below_threshold
Neptunomonas marina	strain=HPM-16	GCA_004005935.1	1815562	1815562	type	True	77.3689	121	1525	95	below_threshold
Nitrincola alkalilacustris	strain=NCAIM B.02612	GCA_008973755.1	1571224	1571224	type	True	77.3551	98	1525	95	below_threshold
Neptunomonas concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	77.3452	110	1525	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	77.3122	151	1525	95	below_threshold
Neptunomonas phycophila	strain=CECT 8716	GCA_001922575.1	1572645	1572645	type	True	77.3057	77	1525	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	77.2848	207	1525	95	below_threshold
Neptunomonas concharum	strain=JCM17730	GCA_008630635.1	1031538	1031538	type	True	77.2708	107	1525	95	below_threshold
Neptunomonas qingdaonensis	strain=P10-2-4	GCA_016082375.1	1045558	1045558	type	True	76.9629	108	1525	95	below_threshold
Neptunomonas qingdaonensis	strain=CGMCC 1.10971	GCA_900113275.1	1045558	1045558	type	True	76.9598	107	1525	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	76.8698	125	1525	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	76.6548	128	1525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:15,923] [INFO] DFAST Taxonomy check result was written to GCF_015209595.1_ASM1520959v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:15,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:15,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:15,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a841599-fe23-4991-826a-d614ccc66216/dqc_reference/checkm_data
[2024-01-24 13:23:15,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:15,974] [INFO] Task started: CheckM
[2024-01-24 13:23:15,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015209595.1_ASM1520959v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015209595.1_ASM1520959v1_genomic.fna/checkm_input GCF_015209595.1_ASM1520959v1_genomic.fna/checkm_result
[2024-01-24 13:23:54,785] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:54,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:54,804] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:54,805] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:54,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015209595.1_ASM1520959v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:54,805] [INFO] Task started: Blastn
[2024-01-24 13:23:54,805] [INFO] Running command: blastn -query GCF_015209595.1_ASM1520959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a841599-fe23-4991-826a-d614ccc66216/dqc_reference/reference_markers_gtdb.fasta -out GCF_015209595.1_ASM1520959v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:55,722] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:55,725] [INFO] Selected 25 target genomes.
[2024-01-24 13:23:55,725] [INFO] Target genome list was writen to GCF_015209595.1_ASM1520959v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:55,755] [INFO] Task started: fastANI
[2024-01-24 13:23:55,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg6642e280-f37a-4567-99d2-d1e8e254cc81/GCF_015209595.1_ASM1520959v1_genomic.fna.gz --refList GCF_015209595.1_ASM1520959v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015209595.1_ASM1520959v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:12,011] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:12,026] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:12,027] [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_015209595.1	s__Pontibacterium sp015209595	100.0	1524	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Pontibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000153345.1	s__Neptuniibacter caesariensis	78.7226	192	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858655.1	s__Amphritea balenae	78.3301	215	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000620085.1	s__Marinobacterium_B jannaschii	78.2509	280	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001597725.1	s__Neptuniibacter marinus	78.241	89	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051665.1	s__Amphritea spongicola	78.2405	181	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435145.1	s__Neptuniibacter sp002435145	77.6416	95	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	99.91	99.87	0.93	0.93	3	-
GCF_001597735.1	s__Neptuniibacter pectenicola	77.6207	124	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	98.78	98.78	0.91	0.91	2	-
GCF_900108065.1	s__Marinobacterium lutimaris	77.5513	129	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067325.1	s__Amphritea sp018067325	77.4859	117	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.51	99.51	0.92	0.92	2	-
GCA_018223185.1	s__Amphritea sp018223185	77.3916	174	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.96	99.96	0.97	0.97	2	-
GCF_004005935.1	s__Neptunomonas marina	77.384	114	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	97.03	97.03	0.93	0.93	2	-
GCF_004339595.1	s__Marinobacterium mangrovicola	77.3559	144	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973755.1	s__Nitrincola alkalilacustris	77.2901	97	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630635.1	s__Neptunomonas concharum	77.2152	104	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	0.98	0.98	2	-
GCF_003014615.1	s__Marinobacterium halophilum	76.9424	141	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.87	98.87	0.91	0.91	2	-
GCF_900113275.1	s__Neptunomonas qingdaonensis	76.9265	105	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000764495.1	s__Nitrincola sp000764495	76.8096	74	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107855.1	s__Marinobacterium georgiense	76.8071	119	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.23	97.23	0.75	0.75	2	-
GCF_014641945.1	s__Marinobacterium zhoushanense	76.5728	126	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:12,029] [INFO] GTDB search result was written to GCF_015209595.1_ASM1520959v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:12,030] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:12,034] [INFO] DFAST_QC result json was written to GCF_015209595.1_ASM1520959v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:12,034] [INFO] DFAST_QC completed!
[2024-01-24 13:24:12,034] [INFO] Total running time: 0h1m31s