[2024-01-24 11:44:23,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,794] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,794] [INFO] DQC Reference Directory: /var/lib/cwl/stgd00b382b-a74f-4cd1-9cb3-de43acb8fa18/dqc_reference
[2024-01-24 11:44:26,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,339] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,340] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bab4177-871e-4193-a8bb-508f368b252e/GCF_016900895.1_ASM1690089v1_genomic.fna.gz | prodigal -d GCF_016900895.1_ASM1690089v1_genomic.fna/cds.fna -a GCF_016900895.1_ASM1690089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:35,608] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:35,608] [INFO] Task started: HMMsearch
[2024-01-24 11:44:35,608] [INFO] Running command: hmmsearch --tblout GCF_016900895.1_ASM1690089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd00b382b-a74f-4cd1-9cb3-de43acb8fa18/dqc_reference/reference_markers.hmm GCF_016900895.1_ASM1690089v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:35,943] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:35,945] [INFO] Found 6/6 markers.
[2024-01-24 11:44:35,988] [INFO] Query marker FASTA was written to GCF_016900895.1_ASM1690089v1_genomic.fna/markers.fasta
[2024-01-24 11:44:35,989] [INFO] Task started: Blastn
[2024-01-24 11:44:35,989] [INFO] Running command: blastn -query GCF_016900895.1_ASM1690089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd00b382b-a74f-4cd1-9cb3-de43acb8fa18/dqc_reference/reference_markers.fasta -out GCF_016900895.1_ASM1690089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:36,766] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:36,769] [INFO] Selected 20 target genomes.
[2024-01-24 11:44:36,769] [INFO] Target genome list was writen to GCF_016900895.1_ASM1690089v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:36,802] [INFO] Task started: fastANI
[2024-01-24 11:44:36,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bab4177-871e-4193-a8bb-508f368b252e/GCF_016900895.1_ASM1690089v1_genomic.fna.gz --refList GCF_016900895.1_ASM1690089v1_genomic.fna/target_genomes.txt --output GCF_016900895.1_ASM1690089v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:56,065] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:56,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd00b382b-a74f-4cd1-9cb3-de43acb8fa18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:56,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd00b382b-a74f-4cd1-9cb3-de43acb8fa18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:56,082] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:56,082] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:56,082] [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
Parashewanella hymeniacidonis	strain=202IG2-18	GCA_016900895.1	2807618	2807618	type	True	100.0	1435	1450	95	conclusive
Parashewanella spongiae	strain=HJ039	GCA_004358345.1	342950	342950	type	True	78.599	310	1450	95	below_threshold
Parashewanella spongiae	strain=KCTC 22492	GCA_003676335.1	342950	342950	type	True	78.5169	291	1450	95	below_threshold
Parashewanella spongiae	strain=KCTC 22492	GCA_023283745.1	342950	342950	type	True	78.4946	289	1450	95	below_threshold
Parashewanella tropica	strain=MEBiC05444	GCA_004358445.1	2547970	2547970	type	True	78.4367	274	1450	95	below_threshold
Parashewanella curva	strain=C51	GCA_003675895.1	2338552	2338552	type	True	78.3222	283	1450	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	78.1133	131	1450	95	below_threshold
Shewanella japonica	strain=KCTC 22435	GCA_002075795.1	93973	93973	type	True	78.0279	156	1450	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	77.9065	164	1450	95	below_threshold
Shewanella halifaxensis	strain=HAW-EB4	GCA_000019185.1	271098	271098	type	True	77.8376	136	1450	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	77.8259	144	1450	95	below_threshold
Shewanella hanedai	strain=JCM 20706	GCA_007197645.1	25	25	type	True	77.8068	129	1450	95	below_threshold
Shewanella hanedai	strain=JCM 20706	GCA_014647575.1	25	25	type	True	77.6892	123	1450	95	below_threshold
Shewanella olleyana	strain=LMG 21437	GCA_023283825.1	135626	135626	type	True	77.6208	159	1450	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	77.6147	148	1450	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	77.5882	138	1450	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	77.4745	152	1450	95	below_threshold
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	77.4634	175	1450	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	77.4178	175	1450	95	below_threshold
Saccharobesus litoralis	strain=CCB-QB4	GCA_003063625.1	2172099	2172099	type	True	76.2069	56	1450	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:56,084] [INFO] DFAST Taxonomy check result was written to GCF_016900895.1_ASM1690089v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:56,085] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:56,085] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:56,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd00b382b-a74f-4cd1-9cb3-de43acb8fa18/dqc_reference/checkm_data
[2024-01-24 11:44:56,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:56,135] [INFO] Task started: CheckM
[2024-01-24 11:44:56,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016900895.1_ASM1690089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016900895.1_ASM1690089v1_genomic.fna/checkm_input GCF_016900895.1_ASM1690089v1_genomic.fna/checkm_result
[2024-01-24 11:45:29,035] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:29,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:29,055] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:29,055] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:29,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016900895.1_ASM1690089v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:29,056] [INFO] Task started: Blastn
[2024-01-24 11:45:29,056] [INFO] Running command: blastn -query GCF_016900895.1_ASM1690089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd00b382b-a74f-4cd1-9cb3-de43acb8fa18/dqc_reference/reference_markers_gtdb.fasta -out GCF_016900895.1_ASM1690089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:30,202] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:30,206] [INFO] Selected 15 target genomes.
[2024-01-24 11:45:30,207] [INFO] Target genome list was writen to GCF_016900895.1_ASM1690089v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:30,216] [INFO] Task started: fastANI
[2024-01-24 11:45:30,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bab4177-871e-4193-a8bb-508f368b252e/GCF_016900895.1_ASM1690089v1_genomic.fna.gz --refList GCF_016900895.1_ASM1690089v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016900895.1_ASM1690089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:46,149] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:46,169] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:46,169] [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_016900895.1	s__Parashewanella sp016900895	100.0	1435	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004168585.1	s__Parashewanella sp004168585	94.0365	1088	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358345.1	s__Parashewanella spongiae	78.5935	311	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004358445.1	s__Parashewanella tropica	78.4116	276	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675895.1	s__Parashewanella curva	78.3365	279	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002873615.1	s__Shewanella sp002873615	78.2776	153	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019525.1	s__Shewanella woodyi	78.0557	125	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.96	97.96	0.94	0.94	2	-
GCF_002075795.1	s__Shewanella japonica	77.9964	158	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.37	97.91	0.95	0.93	6	-
GCF_000019185.1	s__Shewanella halifaxensis	77.8102	136	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197645.1	s__Shewanella hanedai	77.8052	129	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002873135.1	s__Shewanella sp002873135	77.7631	165	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.89	98.82	0.90	0.89	4	-
GCF_009663145.1	s__Shewanella sp009663145	77.6783	149	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648035.1	s__Shewanella algicola	77.5509	156	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_013248905.1	s__Shewanella sp013248905	77.4921	122	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641855.1	s__Shewanella inventionis	77.4683	174	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:46,171] [INFO] GTDB search result was written to GCF_016900895.1_ASM1690089v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:46,172] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:46,177] [INFO] DFAST_QC result json was written to GCF_016900895.1_ASM1690089v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:46,178] [INFO] DFAST_QC completed!
[2024-01-24 11:45:46,178] [INFO] Total running time: 0h1m22s