[2024-01-24 12:06:19,064] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:19,066] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:19,066] [INFO] DQC Reference Directory: /var/lib/cwl/stgffcae6ea-8c65-441a-858e-30d43f3c4975/dqc_reference
[2024-01-24 12:06:20,300] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:20,300] [INFO] Task started: Prodigal
[2024-01-24 12:06:20,301] [INFO] Running command: gunzip -c /var/lib/cwl/stg44f0bb7c-b0f7-4d8e-b12a-0ed26ab3fb77/GCF_002014765.1_ASM201476v1_genomic.fna.gz | prodigal -d GCF_002014765.1_ASM201476v1_genomic.fna/cds.fna -a GCF_002014765.1_ASM201476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:26,416] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:26,417] [INFO] Task started: HMMsearch
[2024-01-24 12:06:26,417] [INFO] Running command: hmmsearch --tblout GCF_002014765.1_ASM201476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffcae6ea-8c65-441a-858e-30d43f3c4975/dqc_reference/reference_markers.hmm GCF_002014765.1_ASM201476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:26,664] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:26,666] [INFO] Found 6/6 markers.
[2024-01-24 12:06:26,692] [INFO] Query marker FASTA was written to GCF_002014765.1_ASM201476v1_genomic.fna/markers.fasta
[2024-01-24 12:06:26,692] [INFO] Task started: Blastn
[2024-01-24 12:06:26,692] [INFO] Running command: blastn -query GCF_002014765.1_ASM201476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffcae6ea-8c65-441a-858e-30d43f3c4975/dqc_reference/reference_markers.fasta -out GCF_002014765.1_ASM201476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:27,284] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:27,287] [INFO] Selected 27 target genomes.
[2024-01-24 12:06:27,288] [INFO] Target genome list was writen to GCF_002014765.1_ASM201476v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:27,298] [INFO] Task started: fastANI
[2024-01-24 12:06:27,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f0bb7c-b0f7-4d8e-b12a-0ed26ab3fb77/GCF_002014765.1_ASM201476v1_genomic.fna.gz --refList GCF_002014765.1_ASM201476v1_genomic.fna/target_genomes.txt --output GCF_002014765.1_ASM201476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:40,814] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:40,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffcae6ea-8c65-441a-858e-30d43f3c4975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:40,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffcae6ea-8c65-441a-858e-30d43f3c4975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:40,830] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:40,830] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:40,831] [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 lincolnii	strain=CCUG 9405	GCA_002014765.1	90241	90241	type	True	100.0	678	679	95	conclusive
Moraxella lacunata	strain=CCUG 4441	GCA_002027545.1	477	477	suspected-type	True	79.7942	130	679	95	below_threshold
Moraxella lacunata	strain=NBRC 102154	GCA_001591245.1	477	477	suspected-type	True	79.7763	116	679	95	below_threshold
Moraxella caprae	strain=NCTC12877	GCA_900453285.1	90240	90240	type	True	77.3855	115	679	95	below_threshold
Moraxella equi	strain=CCUG 4950	GCA_002027555.1	60442	60442	type	True	77.3783	93	679	95	below_threshold
Moraxella equi	strain=NCTC11012	GCA_900453335.1	60442	60442	type	True	77.2883	99	679	95	below_threshold
Moraxella caprae	strain=DSM 19149	GCA_000426885.1	90240	90240	type	True	77.2877	115	679	95	below_threshold
Psychrobacter pygoscelis	strain=I-STPP5b	GCA_004335015.1	2488563	2488563	type	True	76.9258	56	679	95	below_threshold
Moraxella oblonga	strain=NBRC 102422	GCA_001598275.1	200413	200413	type	True	76.908	88	679	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	76.7233	63	679	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	76.623	61	679	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	76.534	58	679	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	76.461	68	679	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	76.4127	62	679	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	76.3077	68	679	95	below_threshold
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	76.1979	58	679	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	76.1798	61	679	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	76.1272	70	679	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:40,832] [INFO] DFAST Taxonomy check result was written to GCF_002014765.1_ASM201476v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:40,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:40,833] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:40,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffcae6ea-8c65-441a-858e-30d43f3c4975/dqc_reference/checkm_data
[2024-01-24 12:06:40,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:40,864] [INFO] Task started: CheckM
[2024-01-24 12:06:40,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002014765.1_ASM201476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002014765.1_ASM201476v1_genomic.fna/checkm_input GCF_002014765.1_ASM201476v1_genomic.fna/checkm_result
[2024-01-24 12:07:06,250] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:06,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:06,273] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:06,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:06,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002014765.1_ASM201476v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:06,274] [INFO] Task started: Blastn
[2024-01-24 12:07:06,275] [INFO] Running command: blastn -query GCF_002014765.1_ASM201476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffcae6ea-8c65-441a-858e-30d43f3c4975/dqc_reference/reference_markers_gtdb.fasta -out GCF_002014765.1_ASM201476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:07,089] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:07,093] [INFO] Selected 29 target genomes.
[2024-01-24 12:07:07,093] [INFO] Target genome list was writen to GCF_002014765.1_ASM201476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:07,124] [INFO] Task started: fastANI
[2024-01-24 12:07:07,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f0bb7c-b0f7-4d8e-b12a-0ed26ab3fb77/GCF_002014765.1_ASM201476v1_genomic.fna.gz --refList GCF_002014765.1_ASM201476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002014765.1_ASM201476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:20,412] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:20,435] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:20,435] [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_002014765.1	s__Moraxella_C lincolnii	100.0	678	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001679005.1	s__Moraxella nonliquefaciens	83.1405	145	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.13	98.18	0.96	0.92	5	-
GCF_001656295.1	s__Moraxella catarrhalis_C	81.9942	120	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.44	97.90	0.94	0.92	5	-
GCF_002027545.1	s__Moraxella lacunata	79.7943	130	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.28	95.16	0.88	0.84	9	-
GCF_000426885.1	s__Moraxella caprae	77.383	113	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	99.99	99.99	1.00	1.00	2	-
GCF_002027555.1	s__Moraxella equi	77.3828	92	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004335015.1	s__Psychrobacter pygoscelis	76.9243	57	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921745.1	s__Psychrobacter sp001921745	76.9166	55	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.15	99.15	0.97	0.97	2	-
GCF_016464015.1	s__Psychrobacter sp016464015	76.8024	83	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_904846155.1	s__Psychrobacter fulvigenes	76.7291	70	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.04	97.04	0.87	0.87	2	-
GCF_017498085.1	s__Psychrobacter sp017498085	76.6909	64	679	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	76.6644	72	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836735.1	s__Psychrobacter sp002836735	76.6504	55	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCF_014192115.1	s__Psychrobacter luti	76.6193	60	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_904846215.1	s__Psychrobacter glacincola_B	76.6	67	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.12	96.12	0.93	0.93	2	-
GCF_000320365.1	s__Moraxella_A macacae	76.5304	90	679	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_000471625.1	s__Psychrobacter aquaticus	76.5286	57	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_904846055.1	s__Psychrobacter ciconiae_A	76.48	71	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163785.1	s__Psychrobacter alimentarius	76.4244	56	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.11	97.08	0.93	0.93	3	-
GCF_002836505.1	s__Psychrobacter sp002836505	76.3886	51	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.96	95.05	0.93	0.86	11	-
GCA_012270355.1	s__Psychrobacter sp012270355	76.3768	77	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836715.1	s__Psychrobacter sp002836715	76.3662	55	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101915.1	s__Psychrobacter pacificensis	76.1979	58	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	98.35	97.54	0.93	0.90	8	-
GCA_002377905.1	s__Psychrobacter sp002377905	75.9689	71	679	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 12:07:20,437] [INFO] GTDB search result was written to GCF_002014765.1_ASM201476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:20,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:20,443] [INFO] DFAST_QC result json was written to GCF_002014765.1_ASM201476v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:20,443] [INFO] DFAST_QC completed!
[2024-01-24 12:07:20,443] [INFO] Total running time: 0h1m1s