[2024-01-24 13:46:10,090] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:10,092] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:10,092] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd839d1a-2f34-40bd-afbd-dbc7751fcf29/dqc_reference
[2024-01-24 13:46:11,325] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:11,326] [INFO] Task started: Prodigal
[2024-01-24 13:46:11,326] [INFO] Running command: gunzip -c /var/lib/cwl/stg2659e0b2-41c1-47e6-a843-7d7360ebb2b7/GCF_021295315.1_ASM2129531v1_genomic.fna.gz | prodigal -d GCF_021295315.1_ASM2129531v1_genomic.fna/cds.fna -a GCF_021295315.1_ASM2129531v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:22,653] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:22,654] [INFO] Task started: HMMsearch
[2024-01-24 13:46:22,654] [INFO] Running command: hmmsearch --tblout GCF_021295315.1_ASM2129531v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd839d1a-2f34-40bd-afbd-dbc7751fcf29/dqc_reference/reference_markers.hmm GCF_021295315.1_ASM2129531v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:23,003] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:23,005] [INFO] Found 6/6 markers.
[2024-01-24 13:46:23,049] [INFO] Query marker FASTA was written to GCF_021295315.1_ASM2129531v1_genomic.fna/markers.fasta
[2024-01-24 13:46:23,050] [INFO] Task started: Blastn
[2024-01-24 13:46:23,050] [INFO] Running command: blastn -query GCF_021295315.1_ASM2129531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd839d1a-2f34-40bd-afbd-dbc7751fcf29/dqc_reference/reference_markers.fasta -out GCF_021295315.1_ASM2129531v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:23,850] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:23,853] [INFO] Selected 24 target genomes.
[2024-01-24 13:46:23,854] [INFO] Target genome list was writen to GCF_021295315.1_ASM2129531v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:23,866] [INFO] Task started: fastANI
[2024-01-24 13:46:23,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg2659e0b2-41c1-47e6-a843-7d7360ebb2b7/GCF_021295315.1_ASM2129531v1_genomic.fna.gz --refList GCF_021295315.1_ASM2129531v1_genomic.fna/target_genomes.txt --output GCF_021295315.1_ASM2129531v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:42,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:42,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd839d1a-2f34-40bd-afbd-dbc7751fcf29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:42,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd839d1a-2f34-40bd-afbd-dbc7751fcf29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:42,364] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:42,364] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:42,364] [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
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	100.0	1547	1550	95	conclusive
Motilimonas eburnea	strain=YH6	GCA_021295345.1	1737488	1737488	type	True	79.9867	564	1550	95	below_threshold
Motilimonas pumila	strain=PLHSC7-2	GCA_003596335.1	2303987	2303987	type	True	79.0481	251	1550	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	77.2887	64	1550	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	77.0697	59	1550	95	below_threshold
Psychromonas aquimarina	strain=ATCC BAA-1526	GCA_000428725.1	444919	444919	type	True	77.0626	72	1550	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	76.8887	65	1550	95	below_threshold
Enterovibrio baiacu	strain=A649	GCA_014863865.1	2491023	2491023	type	True	76.8016	55	1550	95	below_threshold
Enterovibrio baiacu	strain=A649	GCA_004120195.1	2491023	2491023	type	True	76.8016	55	1550	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	76.7811	52	1550	95	below_threshold
Shewanella intestini	strain=MCCC 1A01895	GCA_018221465.1	2017544	2017544	type	True	76.7516	57	1550	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	76.7431	52	1550	95	below_threshold
Photobacterium swingsii	strain=CAIM 1393	GCA_001077885.1	680026	680026	type	True	76.6376	75	1550	95	below_threshold
Photobacterium indicum	strain=ATCC 19614	GCA_003026215.1	81447	81447	type	True	76.6338	71	1550	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	76.62	55	1550	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	76.5684	53	1550	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	76.4812	65	1550	95	below_threshold
Photobacterium frigidiphilum	strain=JCM 12947	GCA_003025615.1	264736	264736	type	True	76.3528	78	1550	95	below_threshold
Grimontia marina	strain=CECT 8713	GCA_900060185.1	646534	646534	type	True	76.2996	51	1550	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	76.1969	65	1550	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:42,366] [INFO] DFAST Taxonomy check result was written to GCF_021295315.1_ASM2129531v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:42,367] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:42,367] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:42,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd839d1a-2f34-40bd-afbd-dbc7751fcf29/dqc_reference/checkm_data
[2024-01-24 13:46:42,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:42,424] [INFO] Task started: CheckM
[2024-01-24 13:46:42,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021295315.1_ASM2129531v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021295315.1_ASM2129531v1_genomic.fna/checkm_input GCF_021295315.1_ASM2129531v1_genomic.fna/checkm_result
[2024-01-24 13:47:19,895] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:19,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:19,917] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:19,918] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:19,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021295315.1_ASM2129531v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:19,919] [INFO] Task started: Blastn
[2024-01-24 13:47:19,919] [INFO] Running command: blastn -query GCF_021295315.1_ASM2129531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd839d1a-2f34-40bd-afbd-dbc7751fcf29/dqc_reference/reference_markers_gtdb.fasta -out GCF_021295315.1_ASM2129531v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:21,091] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:21,096] [INFO] Selected 33 target genomes.
[2024-01-24 13:47:21,097] [INFO] Target genome list was writen to GCF_021295315.1_ASM2129531v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:21,124] [INFO] Task started: fastANI
[2024-01-24 13:47:21,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg2659e0b2-41c1-47e6-a843-7d7360ebb2b7/GCF_021295315.1_ASM2129531v1_genomic.fna.gz --refList GCF_021295315.1_ASM2129531v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021295315.1_ASM2129531v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:44,662] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:44,688] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:47:44,688] [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_003596335.1	s__Motilimonas pumila	79.0321	252	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Motilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004378355.1	s__Psychromonas sp004378355	77.4407	77	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013140855.1	s__Pseudoalteromonas caenipelagi	77.4334	57	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318165.1	s__Psychromonas sp003318165	77.3957	93	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402495.1	s__Pseudoalteromonas sp018402495	77.3027	63	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378715.1	s__Psychromonas sp011378715	77.2522	86	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676025.1	s__Vibrio sp001676025	77.1863	57	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000428725.1	s__Psychromonas aquimarina	77.0608	72	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	76.953	62	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
GCF_000238275.3	s__Pseudoalteromonas undina	76.8258	67	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_018221465.1	s__Shewanella intestini	76.8109	60	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002221505.1	s__Pseudoalteromonas nigrifaciens	76.7999	64	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	98.65	98.00	0.90	0.81	15	-
GCF_000239855.1	s__Pseudoalteromonas sp000239855	76.7993	61	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004120195.1	s__Enterovibrio baiacu	76.7951	54	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003797125.1	s__Shewanella frigidimarina	76.722	61	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_003026215.1	s__Photobacterium indicum	76.6411	72	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196255.1	s__Photobacterium profundum_A	76.6389	70	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.5718	N/A	N/A	N/A	N/A	1	-
GCF_003855155.1	s__Shewanella sp002836275	76.62	55	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.14	98.29	0.96	0.92	3	-
GCF_001077885.1	s__Photobacterium swingsii	76.6173	76	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	76.5638	62	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_014164505.1	s__Shewanella sp014164505	76.537	54	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	76.5111	51	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001465295.1	s__Pseudoalteromonas translucida	76.4501	65	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	N/A	N/A	N/A	N/A	1	-
GCF_003026285.1	s__Photobacterium profundum	76.3997	79	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_003025615.1	s__Photobacterium frigidiphilum	76.3395	77	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.5718	N/A	N/A	N/A	N/A	1	-
GCF_900060185.1	s__Enterovibrio marinus	76.3184	50	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647215.1	s__Shewanella aestuarii	76.2428	63	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214945.1	s__Psychrobium sp013214945	76.2074	64	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:44,690] [INFO] GTDB search result was written to GCF_021295315.1_ASM2129531v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:44,691] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:44,695] [INFO] DFAST_QC result json was written to GCF_021295315.1_ASM2129531v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:44,695] [INFO] DFAST_QC completed!
[2024-01-24 13:47:44,695] [INFO] Total running time: 0h1m35s