[2024-01-24 13:46:28,970] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:28,971] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:28,972] [INFO] DQC Reference Directory: /var/lib/cwl/stga15cdf5d-fcec-4f9e-9298-d4c496f22710/dqc_reference
[2024-01-24 13:46:30,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:30,221] [INFO] Task started: Prodigal
[2024-01-24 13:46:30,221] [INFO] Running command: gunzip -c /var/lib/cwl/stgccdfc2ae-c6fd-460e-8104-374ebb8f9731/GCF_024347235.1_ASM2434723v1_genomic.fna.gz | prodigal -d GCF_024347235.1_ASM2434723v1_genomic.fna/cds.fna -a GCF_024347235.1_ASM2434723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:42,843] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:42,843] [INFO] Task started: HMMsearch
[2024-01-24 13:46:42,843] [INFO] Running command: hmmsearch --tblout GCF_024347235.1_ASM2434723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga15cdf5d-fcec-4f9e-9298-d4c496f22710/dqc_reference/reference_markers.hmm GCF_024347235.1_ASM2434723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:43,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:43,142] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgccdfc2ae-c6fd-460e-8104-374ebb8f9731/GCF_024347235.1_ASM2434723v1_genomic.fna.gz]
[2024-01-24 13:46:43,206] [INFO] Query marker FASTA was written to GCF_024347235.1_ASM2434723v1_genomic.fna/markers.fasta
[2024-01-24 13:46:43,207] [INFO] Task started: Blastn
[2024-01-24 13:46:43,207] [INFO] Running command: blastn -query GCF_024347235.1_ASM2434723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga15cdf5d-fcec-4f9e-9298-d4c496f22710/dqc_reference/reference_markers.fasta -out GCF_024347235.1_ASM2434723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:43,948] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:43,951] [INFO] Selected 26 target genomes.
[2024-01-24 13:46:43,951] [INFO] Target genome list was writen to GCF_024347235.1_ASM2434723v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:44,320] [INFO] Task started: fastANI
[2024-01-24 13:46:44,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgccdfc2ae-c6fd-460e-8104-374ebb8f9731/GCF_024347235.1_ASM2434723v1_genomic.fna.gz --refList GCF_024347235.1_ASM2434723v1_genomic.fna/target_genomes.txt --output GCF_024347235.1_ASM2434723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:02,601] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:02,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga15cdf5d-fcec-4f9e-9298-d4c496f22710/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:02,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga15cdf5d-fcec-4f9e-9298-d4c496f22710/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:02,617] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:02,618] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:02,618] [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
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	99.795	1623	1663	95	conclusive
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	81.9731	1101	1663	95	below_threshold
Amphritea japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	79.0458	207	1663	95	below_threshold
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	78.9823	208	1663	95	below_threshold
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	78.5047	272	1663	95	below_threshold
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	78.4346	283	1663	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	78.3034	160	1663	95	below_threshold
Shewanella amazonensis	strain=SB2B	GCA_000015245.1	60478	60478	type	True	78.2487	58	1663	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	78.2275	236	1663	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	78.0408	238	1663	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	77.3279	159	1663	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	77.1223	136	1663	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	76.8045	109	1663	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	76.654	50	1663	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	76.5932	87	1663	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	76.2737	58	1663	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3882	GCA_001400955.1	251701	251701	pathovar	True	75.9913	55	1663	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	75.7051	53	1663	95	below_threshold
Pseudomonas viridiflava	strain=ICMP 2848	GCA_001642795.1	33069	33069	type	True	75.3526	53	1663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:02,619] [INFO] DFAST Taxonomy check result was written to GCF_024347235.1_ASM2434723v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:02,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:02,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:02,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga15cdf5d-fcec-4f9e-9298-d4c496f22710/dqc_reference/checkm_data
[2024-01-24 13:47:02,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:02,669] [INFO] Task started: CheckM
[2024-01-24 13:47:02,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347235.1_ASM2434723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347235.1_ASM2434723v1_genomic.fna/checkm_input GCF_024347235.1_ASM2434723v1_genomic.fna/checkm_result
[2024-01-24 13:47:45,138] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:45,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:45,169] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:45,169] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:45,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347235.1_ASM2434723v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:45,170] [INFO] Task started: Blastn
[2024-01-24 13:47:45,170] [INFO] Running command: blastn -query GCF_024347235.1_ASM2434723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga15cdf5d-fcec-4f9e-9298-d4c496f22710/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347235.1_ASM2434723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:46,267] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:46,276] [INFO] Selected 28 target genomes.
[2024-01-24 13:47:46,276] [INFO] Target genome list was writen to GCF_024347235.1_ASM2434723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:46,320] [INFO] Task started: fastANI
[2024-01-24 13:47:46,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgccdfc2ae-c6fd-460e-8104-374ebb8f9731/GCF_024347235.1_ASM2434723v1_genomic.fna.gz --refList GCF_024347235.1_ASM2434723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347235.1_ASM2434723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:06,291] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:06,309] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:06,310] [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_017051665.1	s__Amphritea spongicola	99.795	1623	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016592435.1	s__Amphritea japonica	79.0653	209	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018860855.1	s__Amphritea atlantica_A	78.4669	170	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858655.1	s__Amphritea balenae	78.4436	283	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003957515.1	s__Amphritea opalescens	78.318	161	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744155.1	s__Amphritea sp016744155	78.2561	179	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924235.1	s__Amphritea sp016924235	78.2132	234	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCA_018223185.1	s__Amphritea sp018223185	78.1132	242	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.96	99.96	0.97	0.97	2	-
GCF_900111095.1	s__Amphritea atlantica	78.0316	240	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209595.1	s__Pontibacterium sp015209595	77.9834	191	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Pontibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014268445.2	s__Pseudomonas_E sp900187515	77.6688	69	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.07	0.93	0.91	8	-
GCF_900105735.1	s__Pseudomonas_E yamanorum	77.5885	74	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.41	96.42	0.94	0.90	7	-
GCF_001597735.1	s__Neptuniibacter pectenicola	77.3904	72	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	98.78	98.78	0.91	0.91	2	-
GCF_900155945.1	s__Marinobacterium stanieri	77.1665	162	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	96.47	96.47	0.91	0.91	2	-
GCF_000764495.1	s__Nitrincola sp000764495	77.1557	85	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339595.1	s__Marinobacterium mangrovicola	77.1168	137	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084545.1	s__Marinobacterium sp019084545	76.7817	109	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691225.1	s__Nitrincola lacisaponensis	76.5368	87	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373085.1	s__Marinobacterium_A sp013373085	76.0923	99	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642795.1	s__Pseudomonas_E viridiflava	75.3526	53	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	96.41	0.93	0.89	1379	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:06,311] [INFO] GTDB search result was written to GCF_024347235.1_ASM2434723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:06,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:06,316] [INFO] DFAST_QC result json was written to GCF_024347235.1_ASM2434723v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:06,316] [INFO] DFAST_QC completed!
[2024-01-24 13:48:06,316] [INFO] Total running time: 0h1m37s