[2024-01-24 10:57:38,558] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg2516e90b-ace1-4b56-9bf0-483c7362630b/dqc_reference
[2024-01-24 10:57:40,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,030] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,030] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5fd1798-dc67-4e4d-b6a9-bfab4af158e5/GCF_017948405.1_ASM1794840v1_genomic.fna.gz | prodigal -d GCF_017948405.1_ASM1794840v1_genomic.fna/cds.fna -a GCF_017948405.1_ASM1794840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:46,268] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:46,268] [INFO] Task started: HMMsearch
[2024-01-24 10:57:46,269] [INFO] Running command: hmmsearch --tblout GCF_017948405.1_ASM1794840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2516e90b-ace1-4b56-9bf0-483c7362630b/dqc_reference/reference_markers.hmm GCF_017948405.1_ASM1794840v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:46,531] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:46,535] [INFO] Found 6/6 markers.
[2024-01-24 10:57:46,565] [INFO] Query marker FASTA was written to GCF_017948405.1_ASM1794840v1_genomic.fna/markers.fasta
[2024-01-24 10:57:46,566] [INFO] Task started: Blastn
[2024-01-24 10:57:46,566] [INFO] Running command: blastn -query GCF_017948405.1_ASM1794840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2516e90b-ace1-4b56-9bf0-483c7362630b/dqc_reference/reference_markers.fasta -out GCF_017948405.1_ASM1794840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:47,281] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:47,285] [INFO] Selected 23 target genomes.
[2024-01-24 10:57:47,285] [INFO] Target genome list was writen to GCF_017948405.1_ASM1794840v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:47,344] [INFO] Task started: fastANI
[2024-01-24 10:57:47,344] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5fd1798-dc67-4e4d-b6a9-bfab4af158e5/GCF_017948405.1_ASM1794840v1_genomic.fna.gz --refList GCF_017948405.1_ASM1794840v1_genomic.fna/target_genomes.txt --output GCF_017948405.1_ASM1794840v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:01,825] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:01,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2516e90b-ace1-4b56-9bf0-483c7362630b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:01,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2516e90b-ace1-4b56-9bf0-483c7362630b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:01,843] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:01,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:01,843] [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
Psychrosphaera aestuarii	strain=PSC101	GCA_017948405.1	1266052	1266052	type	True	100.0	1014	1016	95	conclusive
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	79.7648	275	1016	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	78.8365	94	1016	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	78.8119	92	1016	95	below_threshold
Psychrosphaera saromensis	strain=SA4-48	GCA_002954545.1	716813	716813	type	True	78.6461	184	1016	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	78.592	69	1016	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	78.3983	88	1016	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	78.262	57	1016	95	below_threshold
Vibrio rumoiensis	strain=FERM P-14531	GCA_002218045.2	76258	76258	type	True	78.2508	59	1016	95	below_threshold
Psychrosphaera saromensis	strain=KCTC 23240	GCA_014652155.1	716813	716813	type	True	78.1388	174	1016	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	77.7059	67	1016	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	77.6884	81	1016	95	below_threshold
Pseudoalteromonas peptidolytica	strain=F12-50-A1	GCA_014858745.1	61150	61150	type	True	77.4057	63	1016	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	76.8715	67	1016	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:01,845] [INFO] DFAST Taxonomy check result was written to GCF_017948405.1_ASM1794840v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:01,846] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:01,846] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:01,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2516e90b-ace1-4b56-9bf0-483c7362630b/dqc_reference/checkm_data
[2024-01-24 10:58:01,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:01,877] [INFO] Task started: CheckM
[2024-01-24 10:58:01,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017948405.1_ASM1794840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017948405.1_ASM1794840v1_genomic.fna/checkm_input GCF_017948405.1_ASM1794840v1_genomic.fna/checkm_result
[2024-01-24 10:58:26,923] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:26,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:26,943] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:26,944] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:26,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017948405.1_ASM1794840v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:26,945] [INFO] Task started: Blastn
[2024-01-24 10:58:26,945] [INFO] Running command: blastn -query GCF_017948405.1_ASM1794840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2516e90b-ace1-4b56-9bf0-483c7362630b/dqc_reference/reference_markers_gtdb.fasta -out GCF_017948405.1_ASM1794840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:28,093] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:28,097] [INFO] Selected 16 target genomes.
[2024-01-24 10:58:28,097] [INFO] Target genome list was writen to GCF_017948405.1_ASM1794840v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:28,110] [INFO] Task started: fastANI
[2024-01-24 10:58:28,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5fd1798-dc67-4e4d-b6a9-bfab4af158e5/GCF_017948405.1_ASM1794840v1_genomic.fna.gz --refList GCF_017948405.1_ASM1794840v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017948405.1_ASM1794840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:38,186] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:38,204] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:38,205] [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_017948405.1	s__Psychrosphaera aestuarii	100.0	1014	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009728465.1	s__Psychrosphaera haliotis	82.3995	547	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017638545.1	s__Psychrosphaera sp017638545	79.7454	276	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197775.1	s__Thalassotalea_A sp007197775	79.5438	50	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954545.1	s__Psychrosphaera saromensis	78.7418	185	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018861025.1	s__Psychrosphaera sp018861025	78.6795	165	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014653195.1	s__Thalassotalea_B profundi	78.592	69	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860345.1	s__Psychrosphaera sp018860345	78.5093	184	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001269985.1	s__Pseudoalteromonas sp001269985	78.2195	89	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.50	95.03	0.90	0.80	3	-
GCF_005886875.1	s__Pseudoalteromonas aurantia_A	77.9361	58	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.47	99.41	0.94	0.93	3	-
GCA_013373245.1	s__Psychrosphaera sp013373245	77.144	123	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590335.1	s__Pseudoalteromonas sp003590335	76.853	56	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.57	97.56	0.90	0.89	3	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	76.0838	81	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:38,207] [INFO] GTDB search result was written to GCF_017948405.1_ASM1794840v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:38,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:38,211] [INFO] DFAST_QC result json was written to GCF_017948405.1_ASM1794840v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:38,212] [INFO] DFAST_QC completed!
[2024-01-24 10:58:38,212] [INFO] Total running time: 0h0m60s