[2024-01-24 13:22:55,343] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:55,345] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:55,345] [INFO] DQC Reference Directory: /var/lib/cwl/stga73f1f65-57b0-4366-8d01-fcb26b38d539/dqc_reference
[2024-01-24 13:22:56,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:56,626] [INFO] Task started: Prodigal
[2024-01-24 13:22:56,626] [INFO] Running command: gunzip -c /var/lib/cwl/stgb84e90dc-4355-423e-b152-fe8b757e4e14/GCF_016028755.1_ASM1602875v1_genomic.fna.gz | prodigal -d GCF_016028755.1_ASM1602875v1_genomic.fna/cds.fna -a GCF_016028755.1_ASM1602875v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:03,647] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:03,647] [INFO] Task started: HMMsearch
[2024-01-24 13:23:03,648] [INFO] Running command: hmmsearch --tblout GCF_016028755.1_ASM1602875v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga73f1f65-57b0-4366-8d01-fcb26b38d539/dqc_reference/reference_markers.hmm GCF_016028755.1_ASM1602875v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:03,889] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:03,890] [INFO] Found 6/6 markers.
[2024-01-24 13:23:03,918] [INFO] Query marker FASTA was written to GCF_016028755.1_ASM1602875v1_genomic.fna/markers.fasta
[2024-01-24 13:23:03,918] [INFO] Task started: Blastn
[2024-01-24 13:23:03,918] [INFO] Running command: blastn -query GCF_016028755.1_ASM1602875v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga73f1f65-57b0-4366-8d01-fcb26b38d539/dqc_reference/reference_markers.fasta -out GCF_016028755.1_ASM1602875v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:04,575] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:04,584] [INFO] Selected 15 target genomes.
[2024-01-24 13:23:04,585] [INFO] Target genome list was writen to GCF_016028755.1_ASM1602875v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:04,605] [INFO] Task started: fastANI
[2024-01-24 13:23:04,606] [INFO] Running command: fastANI --query /var/lib/cwl/stgb84e90dc-4355-423e-b152-fe8b757e4e14/GCF_016028755.1_ASM1602875v1_genomic.fna.gz --refList GCF_016028755.1_ASM1602875v1_genomic.fna/target_genomes.txt --output GCF_016028755.1_ASM1602875v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:13,485] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:13,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga73f1f65-57b0-4366-8d01-fcb26b38d539/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:13,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga73f1f65-57b0-4366-8d01-fcb26b38d539/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:13,496] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:23:13,496] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:13,497] [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
Moraxella osloensis	strain=FDAARGOS_870	GCA_016028755.1	34062	34062	suspected-type	True	100.0	811	811	95	conclusive
Moraxella osloensis	strain=NCTC10465	GCA_900453115.1	34062	34062	suspected-type	True	99.9982	808	811	95	conclusive
Moraxella osloensis	strain=CCUG 350	GCA_001553955.1	34062	34062	suspected-type	True	99.996	810	811	95	conclusive
Moraxella osloensis	strain=CCUG 350	GCA_001679175.1	34062	34062	suspected-type	True	99.9542	767	811	95	conclusive
Moraxella boevrei	strain=DSM 14165	GCA_000379845.1	346665	346665	type	True	77.5452	151	811	95	below_threshold
Moraxella caviae	strain=NCTC10293	GCA_900453175.1	34060	34060	type	True	77.511	81	811	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	76.7542	67	811	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	76.7225	89	811	95	below_threshold
Moraxella pluranimalium	strain=CCUG 54913	GCA_002014825.1	470453	470453	type	True	76.5394	91	811	95	below_threshold
Psychrobacter phenylpyruvicus	strain=NBRC 102152	GCA_001591185.1	29432	29432	type	True	76.5281	70	811	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	76.3944	81	811	95	below_threshold
Psychrobacter frigidicola	strain=ACAM 304	GCA_007997305.1	45611	45611	type	True	76.231	57	811	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:13,498] [INFO] DFAST Taxonomy check result was written to GCF_016028755.1_ASM1602875v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:13,499] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:13,499] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:13,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga73f1f65-57b0-4366-8d01-fcb26b38d539/dqc_reference/checkm_data
[2024-01-24 13:23:13,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:13,535] [INFO] Task started: CheckM
[2024-01-24 13:23:13,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016028755.1_ASM1602875v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016028755.1_ASM1602875v1_genomic.fna/checkm_input GCF_016028755.1_ASM1602875v1_genomic.fna/checkm_result
[2024-01-24 13:23:39,246] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:39,247] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:39,265] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:39,265] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:39,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016028755.1_ASM1602875v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:39,266] [INFO] Task started: Blastn
[2024-01-24 13:23:39,266] [INFO] Running command: blastn -query GCF_016028755.1_ASM1602875v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga73f1f65-57b0-4366-8d01-fcb26b38d539/dqc_reference/reference_markers_gtdb.fasta -out GCF_016028755.1_ASM1602875v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:40,313] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:40,320] [INFO] Selected 16 target genomes.
[2024-01-24 13:23:40,320] [INFO] Target genome list was writen to GCF_016028755.1_ASM1602875v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:40,360] [INFO] Task started: fastANI
[2024-01-24 13:23:40,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgb84e90dc-4355-423e-b152-fe8b757e4e14/GCF_016028755.1_ASM1602875v1_genomic.fna.gz --refList GCF_016028755.1_ASM1602875v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016028755.1_ASM1602875v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:48,563] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:48,580] [INFO] Found 16 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:23:48,580] [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_001553955.1	s__Moraxella_A osloensis	99.9961	809	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0237	96.88	95.23	0.89	0.83	12	inconclusive
GCF_009867135.1	s__Moraxella_A sp002478835	95.0813	724	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0237	96.28	95.11	0.93	0.88	7	inconclusive
GCA_014647715.1	s__Moraxella_A cinereus	94.8741	713	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0	95.56	95.32	0.87	0.85	40	-
GCF_904846145.1	s__Psychrobacter immobilis_G	78.8221	72	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591265.1	s__Moraxella_A atlantae	78.3966	180	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0	98.57	96.98	0.93	0.88	5	-
GCF_000320365.1	s__Moraxella_A macacae	78.2507	107	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379845.1	s__Moraxella_A boevrei	77.5353	151	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725675.1	s__Psychrobacter sanguinis_A	77.3046	70	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.56	98.43	0.91	0.90	4	-
GCF_016464015.1	s__Psychrobacter sp016464015	77.0663	91	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002014855.1	s__Moraxella porci	76.9759	65	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.21	96.21	0.92	0.92	2	-
GCF_016107555.1	s__Psychrobacter celer	76.7042	81	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.12	95.68	0.88	0.85	9	-
GCF_002014825.1	s__Moraxella pluranimalium	76.5394	91	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277735.1	s__Psychrobacter sp015277735	76.5033	70	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.26	95.15	0.92	0.92	3	-
GCF_002014985.1	s__Moraxella caviae	76.4686	74	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.91	99.82	0.90	0.81	3	-
GCF_016107575.1	s__Psychrobacter faecalis	76.4255	101	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.81	95.77	0.89	0.85	16	-
GCA_002414005.1	s__Psychrobacter sp002414005	76.1637	85	811	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 13:23:48,581] [INFO] GTDB search result was written to GCF_016028755.1_ASM1602875v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:48,582] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:48,585] [INFO] DFAST_QC result json was written to GCF_016028755.1_ASM1602875v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:48,586] [INFO] DFAST_QC completed!
[2024-01-24 13:23:48,586] [INFO] Total running time: 0h0m53s