[2024-01-24 12:42:09,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg091b8215-1ba6-4efc-8cbf-8e2d25e60337/dqc_reference
[2024-01-24 12:42:10,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,830] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,831] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5505099-d752-42dc-aab4-da7fcd62b71f/GCF_023284045.1_ASM2328404v1_genomic.fna.gz | prodigal -d GCF_023284045.1_ASM2328404v1_genomic.fna/cds.fna -a GCF_023284045.1_ASM2328404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:21,831] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:21,831] [INFO] Task started: HMMsearch
[2024-01-24 12:42:21,832] [INFO] Running command: hmmsearch --tblout GCF_023284045.1_ASM2328404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg091b8215-1ba6-4efc-8cbf-8e2d25e60337/dqc_reference/reference_markers.hmm GCF_023284045.1_ASM2328404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:22,166] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:22,168] [INFO] Found 6/6 markers.
[2024-01-24 12:42:22,213] [INFO] Query marker FASTA was written to GCF_023284045.1_ASM2328404v1_genomic.fna/markers.fasta
[2024-01-24 12:42:22,213] [INFO] Task started: Blastn
[2024-01-24 12:42:22,213] [INFO] Running command: blastn -query GCF_023284045.1_ASM2328404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg091b8215-1ba6-4efc-8cbf-8e2d25e60337/dqc_reference/reference_markers.fasta -out GCF_023284045.1_ASM2328404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:22,980] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:22,984] [INFO] Selected 12 target genomes.
[2024-01-24 12:42:22,984] [INFO] Target genome list was writen to GCF_023284045.1_ASM2328404v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:22,990] [INFO] Task started: fastANI
[2024-01-24 12:42:22,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5505099-d752-42dc-aab4-da7fcd62b71f/GCF_023284045.1_ASM2328404v1_genomic.fna.gz --refList GCF_023284045.1_ASM2328404v1_genomic.fna/target_genomes.txt --output GCF_023284045.1_ASM2328404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:35,961] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:35,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg091b8215-1ba6-4efc-8cbf-8e2d25e60337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:35,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg091b8215-1ba6-4efc-8cbf-8e2d25e60337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:35,972] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:42:35,972] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:35,972] [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
Shewanella kaireitica	strain=DSM 17170	GCA_023284045.1	212021	212021	type	True	100.0	1668	1670	95	conclusive
Shewanella piezotolerans	strain=WP3	GCA_000014885.1	404011	404011	type	True	91.7943	1496	1670	95	below_threshold
Shewanella gelidimarina	strain=ATCC 700752	GCA_023283945.1	56813	56813	type	True	81.5751	952	1670	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	81.4735	940	1670	95	below_threshold
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	80.2256	599	1670	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	80.0603	642	1670	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	79.8874	651	1670	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_019654995.1	190308	190308	type	True	79.8677	643	1670	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	79.825	642	1670	95	below_threshold
Shewanella eurypsychrophilus	strain=YLB-08	GCA_007004545.3	2593656	2593656	type	True	78.7045	387	1670	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	78.2626	239	1670	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	77.8007	234	1670	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:35,974] [INFO] DFAST Taxonomy check result was written to GCF_023284045.1_ASM2328404v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:35,974] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:35,975] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:35,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg091b8215-1ba6-4efc-8cbf-8e2d25e60337/dqc_reference/checkm_data
[2024-01-24 12:42:35,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:36,024] [INFO] Task started: CheckM
[2024-01-24 12:42:36,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023284045.1_ASM2328404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023284045.1_ASM2328404v1_genomic.fna/checkm_input GCF_023284045.1_ASM2328404v1_genomic.fna/checkm_result
[2024-01-24 12:43:12,915] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:12,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:12,940] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:12,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:12,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023284045.1_ASM2328404v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:12,941] [INFO] Task started: Blastn
[2024-01-24 12:43:12,941] [INFO] Running command: blastn -query GCF_023284045.1_ASM2328404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg091b8215-1ba6-4efc-8cbf-8e2d25e60337/dqc_reference/reference_markers_gtdb.fasta -out GCF_023284045.1_ASM2328404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:14,080] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:14,083] [INFO] Selected 11 target genomes.
[2024-01-24 12:43:14,083] [INFO] Target genome list was writen to GCF_023284045.1_ASM2328404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:14,091] [INFO] Task started: fastANI
[2024-01-24 12:43:14,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5505099-d752-42dc-aab4-da7fcd62b71f/GCF_023284045.1_ASM2328404v1_genomic.fna.gz --refList GCF_023284045.1_ASM2328404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023284045.1_ASM2328404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:26,563] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:26,583] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:43:26,583] [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_000014885.1	s__Shewanella piezotolerans	91.7844	1497	1670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757755.1	s__Shewanella sp016757755	81.7841	1002	1670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836205.1	s__Shewanella sp002836205	81.4195	996	1670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.46	99.13	0.96	0.92	4	-
GCF_000018285.1	s__Shewanella pealeana	80.0205	617	1670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019185.1	s__Shewanella halifaxensis	80.0156	623	1670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765635.1	s__Shewanella schlegeliana	79.9008	649	1670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518605.1	s__Shewanella fidelis	79.7133	605	1670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_000018025.1	s__Shewanella sediminis	78.8928	385	1670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004545.2	s__Shewanella sp007004545	78.8107	376	1670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.97	99.97	0.99	0.99	2	-
GCF_002873615.1	s__Shewanella sp002873615	77.9677	302	1670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855395.1	s__Shewanella livingstonensis	77.7856	224	1670	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 12:43:26,585] [INFO] GTDB search result was written to GCF_023284045.1_ASM2328404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:26,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:26,590] [INFO] DFAST_QC result json was written to GCF_023284045.1_ASM2328404v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:26,591] [INFO] DFAST_QC completed!
[2024-01-24 12:43:26,591] [INFO] Total running time: 0h1m17s