[2024-01-24 14:23:16,610] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:16,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:16,612] [INFO] DQC Reference Directory: /var/lib/cwl/stg31fcf369-e096-4d3a-a50a-75130469178b/dqc_reference
[2024-01-24 14:23:17,868] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:17,869] [INFO] Task started: Prodigal
[2024-01-24 14:23:17,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fcd3c1f-d2bb-4d1e-b09d-bce793d6a5a0/GCF_014192115.1_ASM1419211v1_genomic.fna.gz | prodigal -d GCF_014192115.1_ASM1419211v1_genomic.fna/cds.fna -a GCF_014192115.1_ASM1419211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:24,866] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:24,867] [INFO] Task started: HMMsearch
[2024-01-24 14:23:24,867] [INFO] Running command: hmmsearch --tblout GCF_014192115.1_ASM1419211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31fcf369-e096-4d3a-a50a-75130469178b/dqc_reference/reference_markers.hmm GCF_014192115.1_ASM1419211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:25,191] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:25,193] [INFO] Found 6/6 markers.
[2024-01-24 14:23:25,219] [INFO] Query marker FASTA was written to GCF_014192115.1_ASM1419211v1_genomic.fna/markers.fasta
[2024-01-24 14:23:25,220] [INFO] Task started: Blastn
[2024-01-24 14:23:25,220] [INFO] Running command: blastn -query GCF_014192115.1_ASM1419211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31fcf369-e096-4d3a-a50a-75130469178b/dqc_reference/reference_markers.fasta -out GCF_014192115.1_ASM1419211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:25,920] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:25,924] [INFO] Selected 14 target genomes.
[2024-01-24 14:23:25,924] [INFO] Target genome list was writen to GCF_014192115.1_ASM1419211v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:25,938] [INFO] Task started: fastANI
[2024-01-24 14:23:25,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fcd3c1f-d2bb-4d1e-b09d-bce793d6a5a0/GCF_014192115.1_ASM1419211v1_genomic.fna.gz --refList GCF_014192115.1_ASM1419211v1_genomic.fna/target_genomes.txt --output GCF_014192115.1_ASM1419211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:36,784] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:36,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31fcf369-e096-4d3a-a50a-75130469178b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:36,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31fcf369-e096-4d3a-a50a-75130469178b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:36,796] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:36,796] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:36,796] [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 luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	100.0	981	982	95	conclusive
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	85.7374	764	982	95	below_threshold
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	85.5104	791	982	95	below_threshold
Psychrobacter cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	83.0315	729	982	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	82.6964	723	982	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	82.6256	716	982	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	82.5951	628	982	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	82.3082	708	982	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	81.4536	648	982	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	80.6084	620	982	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	80.4197	584	982	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	80.3958	573	982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:36,798] [INFO] DFAST Taxonomy check result was written to GCF_014192115.1_ASM1419211v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:36,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:36,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:36,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31fcf369-e096-4d3a-a50a-75130469178b/dqc_reference/checkm_data
[2024-01-24 14:23:36,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:36,831] [INFO] Task started: CheckM
[2024-01-24 14:23:36,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192115.1_ASM1419211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192115.1_ASM1419211v1_genomic.fna/checkm_input GCF_014192115.1_ASM1419211v1_genomic.fna/checkm_result
[2024-01-24 14:24:05,663] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:05,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:05,685] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:05,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:05,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192115.1_ASM1419211v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:05,686] [INFO] Task started: Blastn
[2024-01-24 14:24:05,686] [INFO] Running command: blastn -query GCF_014192115.1_ASM1419211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31fcf369-e096-4d3a-a50a-75130469178b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192115.1_ASM1419211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:06,804] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:06,808] [INFO] Selected 11 target genomes.
[2024-01-24 14:24:06,808] [INFO] Target genome list was writen to GCF_014192115.1_ASM1419211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:06,818] [INFO] Task started: fastANI
[2024-01-24 14:24:06,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fcd3c1f-d2bb-4d1e-b09d-bce793d6a5a0/GCF_014192115.1_ASM1419211v1_genomic.fna.gz --refList GCF_014192115.1_ASM1419211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192115.1_ASM1419211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:14,982] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:14,996] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:14,996] [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_014192115.1	s__Psychrobacter luti	100.0	981	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_904846345.1	s__Psychrobacter maritimus	91.7153	875	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.41	96.16	0.91	0.90	6	-
GCF_904846285.1	s__Psychrobacter immobilis_D	89.4215	841	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846175.1	s__Psychrobacter immobilis_E	89.4073	853	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369115.1	s__Psychrobacter sp008369115	88.8861	862	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013905.1	s__Psychrobacter cryohalolentis	83.0315	729	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.64	96.60	0.93	0.89	9	-
GCF_904846525.1	s__Psychrobacter sp904846525	82.6334	723	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3008	N/A	N/A	N/A	N/A	1	-
GCF_904846615.1	s__Psychrobacter sp000586455	82.616	717	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4083	99.93	99.93	1.00	1.00	2	-
GCF_904846075.1	s__Psychrobacter glacincola_C	82.5985	722	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	96.53	96.53	0.88	0.88	2	-
GCF_900168255.1	s__Psychrobacter sp900168255	82.5492	734	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.48	96.48	0.91	0.91	2	-
GCF_904846225.1	s__Psychrobacter immobilis_F	80.5969	638	982	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 14:24:14,998] [INFO] GTDB search result was written to GCF_014192115.1_ASM1419211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:14,999] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:15,004] [INFO] DFAST_QC result json was written to GCF_014192115.1_ASM1419211v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:15,005] [INFO] DFAST_QC completed!
[2024-01-24 14:24:15,005] [INFO] Total running time: 0h0m58s