[2024-01-24 14:22:01,248] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,250] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,250] [INFO] DQC Reference Directory: /var/lib/cwl/stg57e4a12b-8504-4d26-afe6-df0e319ab4d4/dqc_reference
[2024-01-24 14:22:02,597] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,600] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eff375e-428d-4da4-9ce2-afc0fadf0bb3/GCF_004335015.1_ASM433501v1_genomic.fna.gz | prodigal -d GCF_004335015.1_ASM433501v1_genomic.fna/cds.fna -a GCF_004335015.1_ASM433501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:10,336] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:10,336] [INFO] Task started: HMMsearch
[2024-01-24 14:22:10,337] [INFO] Running command: hmmsearch --tblout GCF_004335015.1_ASM433501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57e4a12b-8504-4d26-afe6-df0e319ab4d4/dqc_reference/reference_markers.hmm GCF_004335015.1_ASM433501v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:10,623] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:10,624] [INFO] Found 6/6 markers.
[2024-01-24 14:22:10,652] [INFO] Query marker FASTA was written to GCF_004335015.1_ASM433501v1_genomic.fna/markers.fasta
[2024-01-24 14:22:10,652] [INFO] Task started: Blastn
[2024-01-24 14:22:10,653] [INFO] Running command: blastn -query GCF_004335015.1_ASM433501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e4a12b-8504-4d26-afe6-df0e319ab4d4/dqc_reference/reference_markers.fasta -out GCF_004335015.1_ASM433501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:11,373] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:11,377] [INFO] Selected 26 target genomes.
[2024-01-24 14:22:11,377] [INFO] Target genome list was writen to GCF_004335015.1_ASM433501v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:11,412] [INFO] Task started: fastANI
[2024-01-24 14:22:11,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eff375e-428d-4da4-9ce2-afc0fadf0bb3/GCF_004335015.1_ASM433501v1_genomic.fna.gz --refList GCF_004335015.1_ASM433501v1_genomic.fna/target_genomes.txt --output GCF_004335015.1_ASM433501v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:26,312] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:26,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57e4a12b-8504-4d26-afe6-df0e319ab4d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:26,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57e4a12b-8504-4d26-afe6-df0e319ab4d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:26,329] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:26,329] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:26,329] [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 pygoscelis	strain=I-STPP5b	GCA_004335015.1	2488563	2488563	type	True	100.0	1125	1126	95	conclusive
Psychrobacter cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	77.7875	162	1126	95	below_threshold
Psychrobacter sanguinis	strain=FDAARGOS_1598	GCA_020736705.1	861445	861445	type	True	77.6925	122	1126	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	77.5896	178	1126	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	77.5576	159	1126	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	77.5446	159	1126	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	77.5338	161	1126	95	below_threshold
Psychrobacter phenylpyruvicus	strain=NCTC10526	GCA_900455955.1	29432	29432	type	True	77.4973	114	1126	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	77.4855	155	1126	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	77.4824	162	1126	95	below_threshold
Psychrobacter phenylpyruvicus	strain=DSM 7000	GCA_000685805.1	29432	29432	type	True	77.4595	113	1126	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	77.4409	191	1126	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	77.4273	153	1126	95	below_threshold
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	77.3378	161	1126	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	77.2206	164	1126	95	below_threshold
Psychrobacter phenylpyruvicus	strain=NBRC 102152	GCA_001591185.1	29432	29432	type	True	77.2125	102	1126	95	below_threshold
Psychrobacter frigidicola	strain=ACAM 304	GCA_007997305.1	45611	45611	type	True	77.1586	166	1126	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	77.155	194	1126	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	77.0463	188	1126	95	below_threshold
Psychrobacter lutiphocae	strain=DSM 21542	GCA_000382145.1	540500	540500	type	True	76.8627	124	1126	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:26,331] [INFO] DFAST Taxonomy check result was written to GCF_004335015.1_ASM433501v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:26,332] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:26,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:26,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57e4a12b-8504-4d26-afe6-df0e319ab4d4/dqc_reference/checkm_data
[2024-01-24 14:22:26,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:26,371] [INFO] Task started: CheckM
[2024-01-24 14:22:26,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004335015.1_ASM433501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004335015.1_ASM433501v1_genomic.fna/checkm_input GCF_004335015.1_ASM433501v1_genomic.fna/checkm_result
[2024-01-24 14:22:54,377] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:54,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:54,408] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:54,409] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:54,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004335015.1_ASM433501v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:54,410] [INFO] Task started: Blastn
[2024-01-24 14:22:54,410] [INFO] Running command: blastn -query GCF_004335015.1_ASM433501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e4a12b-8504-4d26-afe6-df0e319ab4d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_004335015.1_ASM433501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:55,486] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:55,492] [INFO] Selected 23 target genomes.
[2024-01-24 14:22:55,493] [INFO] Target genome list was writen to GCF_004335015.1_ASM433501v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:55,527] [INFO] Task started: fastANI
[2024-01-24 14:22:55,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eff375e-428d-4da4-9ce2-afc0fadf0bb3/GCF_004335015.1_ASM433501v1_genomic.fna.gz --refList GCF_004335015.1_ASM433501v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004335015.1_ASM433501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:08,417] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:08,442] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:08,442] [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_004335015.1	s__Psychrobacter pygoscelis	100.0	1125	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_904848165.1	s__Psychrobacter arenosus	78.7192	337	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846035.1	s__Psychrobacter aestuarii	77.7367	151	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435845.1	s__Psychrobacter sp001435845	77.6526	172	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846685.1	s__Psychrobacter sp000511655	77.5151	178	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.68	97.54	0.87	0.80	6	-
GCF_016107545.1	s__Psychrobacter namhaensis	77.4758	161	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.25	97.66	0.93	0.91	5	-
GCF_003350005.1	s__Psychrobacter proteolyticus_A	77.4657	173	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.98	99.95	0.99	0.99	4	-
GCF_000685805.1	s__Psychrobacter phenylpyruvicus	77.4534	114	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	99.99	1.00	0.99	4	-
GCF_002836735.1	s__Psychrobacter sp002836735	77.4472	169	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCF_016107555.1	s__Psychrobacter celer	77.4409	191	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.12	95.68	0.88	0.85	9	-
GCF_003217155.1	s__Psychrobacter fozii	77.4259	153	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.56	95.06	0.91	0.88	5	-
GCF_013248965.1	s__Psychrobacter okhotskensis	77.4041	197	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.29	97.15	0.88	0.85	12	-
GCF_904846625.1	s__Psychrobacter sp000586415	77.3977	184	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.91	99.91	1.00	1.00	2	-
GCF_904846185.1	s__Psychrobacter immobilis_B	77.3745	171	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3523	99.90	99.90	0.97	0.97	2	-
GCF_904846315.1	s__Psychrobacter jeotgali	77.3671	175	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014861365.1	s__Psychrobacter sp014861365	77.3667	171	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.77	98.77	0.85	0.85	2	-
GCF_001298525.1	s__Psychrobacter urativorans_A	77.3262	151	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846055.1	s__Psychrobacter ciconiae_A	77.3184	120	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014861395.1	s__Psychrobacter sp014861395	77.2994	151	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.67	98.67	0.84	0.84	2	-
GCF_904846705.1	s__Psychrobacter sp904846705	77.1064	173	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414005.1	s__Psychrobacter sp002414005	77.0798	170	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652895.1	s__Psychrobacter glaciei	77.0673	189	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.25	96.04	0.92	0.86	6	-
GCA_002377945.1	s__Psychrobacter sp002377945	77.0258	181	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:08,444] [INFO] GTDB search result was written to GCF_004335015.1_ASM433501v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:08,444] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:08,449] [INFO] DFAST_QC result json was written to GCF_004335015.1_ASM433501v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:08,449] [INFO] DFAST_QC completed!
[2024-01-24 14:23:08,449] [INFO] Total running time: 0h1m7s