[2024-01-24 11:35:11,955] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,973] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,973] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2fc5581-6729-4359-bae2-c5d2220b5459/dqc_reference
[2024-01-24 11:35:14,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:14,465] [INFO] Task started: Prodigal
[2024-01-24 11:35:14,465] [INFO] Running command: gunzip -c /var/lib/cwl/stg720a7dfb-2e08-46f1-833a-d58157c1440f/GCF_003148585.1_ASM314858v1_genomic.fna.gz | prodigal -d GCF_003148585.1_ASM314858v1_genomic.fna/cds.fna -a GCF_003148585.1_ASM314858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:21,962] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:21,963] [INFO] Task started: HMMsearch
[2024-01-24 11:35:21,963] [INFO] Running command: hmmsearch --tblout GCF_003148585.1_ASM314858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2fc5581-6729-4359-bae2-c5d2220b5459/dqc_reference/reference_markers.hmm GCF_003148585.1_ASM314858v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:22,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:22,244] [INFO] Found 6/6 markers.
[2024-01-24 11:35:22,271] [INFO] Query marker FASTA was written to GCF_003148585.1_ASM314858v1_genomic.fna/markers.fasta
[2024-01-24 11:35:22,271] [INFO] Task started: Blastn
[2024-01-24 11:35:22,271] [INFO] Running command: blastn -query GCF_003148585.1_ASM314858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2fc5581-6729-4359-bae2-c5d2220b5459/dqc_reference/reference_markers.fasta -out GCF_003148585.1_ASM314858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:22,954] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:22,957] [INFO] Selected 15 target genomes.
[2024-01-24 11:35:22,957] [INFO] Target genome list was writen to GCF_003148585.1_ASM314858v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:22,967] [INFO] Task started: fastANI
[2024-01-24 11:35:22,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg720a7dfb-2e08-46f1-833a-d58157c1440f/GCF_003148585.1_ASM314858v1_genomic.fna.gz --refList GCF_003148585.1_ASM314858v1_genomic.fna/target_genomes.txt --output GCF_003148585.1_ASM314858v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:34,283] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:34,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2fc5581-6729-4359-bae2-c5d2220b5459/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:34,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2fc5581-6729-4359-bae2-c5d2220b5459/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:34,297] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:34,297] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:35:34,297] [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
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	100.0	1059	1062	95	inconclusive
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	96.3161	939	1062	95	inconclusive
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	91.2613	927	1062	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	83.3707	796	1062	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	82.8227	771	1062	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	82.7478	718	1062	95	below_threshold
Psychrobacter cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	82.5255	675	1062	95	below_threshold
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	81.9703	662	1062	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	81.9673	667	1062	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	81.8901	717	1062	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	81.7234	602	1062	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	80.9853	615	1062	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	80.6019	639	1062	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:34,301] [INFO] DFAST Taxonomy check result was written to GCF_003148585.1_ASM314858v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:34,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:34,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:34,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2fc5581-6729-4359-bae2-c5d2220b5459/dqc_reference/checkm_data
[2024-01-24 11:35:34,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:34,340] [INFO] Task started: CheckM
[2024-01-24 11:35:34,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003148585.1_ASM314858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003148585.1_ASM314858v1_genomic.fna/checkm_input GCF_003148585.1_ASM314858v1_genomic.fna/checkm_result
[2024-01-24 11:36:03,074] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:03,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:03,095] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:03,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:03,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003148585.1_ASM314858v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:03,097] [INFO] Task started: Blastn
[2024-01-24 11:36:03,097] [INFO] Running command: blastn -query GCF_003148585.1_ASM314858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2fc5581-6729-4359-bae2-c5d2220b5459/dqc_reference/reference_markers_gtdb.fasta -out GCF_003148585.1_ASM314858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:04,159] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:04,162] [INFO] Selected 12 target genomes.
[2024-01-24 11:36:04,162] [INFO] Target genome list was writen to GCF_003148585.1_ASM314858v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:04,190] [INFO] Task started: fastANI
[2024-01-24 11:36:04,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg720a7dfb-2e08-46f1-833a-d58157c1440f/GCF_003148585.1_ASM314858v1_genomic.fna.gz --refList GCF_003148585.1_ASM314858v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003148585.1_ASM314858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:13,829] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:13,839] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:13,839] [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_003148585.1	s__Psychrobacter immobilis	100.0	1059	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3742	98.07	96.42	0.95	0.91	4	conclusive
GCF_904846615.1	s__Psychrobacter sp000586455	96.3742	975	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4083	99.93	99.93	1.00	1.00	2	-
GCA_904846265.1	s__Psychrobacter immobilis_A	96.3627	951	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3849	97.94	96.82	0.94	0.90	4	-
GCA_001411745.2	s__Psychrobacter glacincola_A	96.3409	961	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	N/A	N/A	N/A	N/A	1	-
GCF_904846075.1	s__Psychrobacter glacincola_C	96.3188	968	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	96.53	96.53	0.88	0.88	2	-
GCF_904846185.1	s__Psychrobacter immobilis_B	96.3038	969	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3523	99.90	99.90	0.97	0.97	2	-
GCF_016107535.1	s__Psychrobacter cibarius	96.2928	940	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3915	99.97	99.97	0.99	0.99	2	-
GCF_001435295.1	s__Psychrobacter sp001435295	96.2682	976	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4083	N/A	N/A	N/A	N/A	1	-
GCF_904846525.1	s__Psychrobacter sp904846525	96.2525	949	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3008	N/A	N/A	N/A	N/A	1	-
GCF_000586475.1	s__Psychrobacter sp000586475	96.1928	962	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2677	98.16	96.39	0.95	0.90	3	-
GCA_018448495.1	s__Psychrobacter sp018448495	96.1541	976	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.24	97.46	97.46	0.95	0.95	2	-
GCF_014897815.1	s__Psychrobacter sp003530515	95.9083	952	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2297	99.71	99.49	0.97	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:13,841] [INFO] GTDB search result was written to GCF_003148585.1_ASM314858v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:13,842] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:13,845] [INFO] DFAST_QC result json was written to GCF_003148585.1_ASM314858v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:13,845] [INFO] DFAST_QC completed!
[2024-01-24 11:36:13,845] [INFO] Total running time: 0h1m2s