[2024-01-25 19:10:20,777] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:20,778] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:20,779] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d0ea6a0-9bdc-4d5e-b3a6-ca5271715cda/dqc_reference
[2024-01-25 19:10:21,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:21,934] [INFO] Task started: Prodigal
[2024-01-25 19:10:21,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d37560f-e2d6-4e54-8204-5c616726b2c1/GCF_000379845.1_ASM37984v1_genomic.fna.gz | prodigal -d GCF_000379845.1_ASM37984v1_genomic.fna/cds.fna -a GCF_000379845.1_ASM37984v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:27,470] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:27,470] [INFO] Task started: HMMsearch
[2024-01-25 19:10:27,470] [INFO] Running command: hmmsearch --tblout GCF_000379845.1_ASM37984v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d0ea6a0-9bdc-4d5e-b3a6-ca5271715cda/dqc_reference/reference_markers.hmm GCF_000379845.1_ASM37984v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:27,651] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:27,652] [INFO] Found 6/6 markers.
[2024-01-25 19:10:27,672] [INFO] Query marker FASTA was written to GCF_000379845.1_ASM37984v1_genomic.fna/markers.fasta
[2024-01-25 19:10:27,672] [INFO] Task started: Blastn
[2024-01-25 19:10:27,672] [INFO] Running command: blastn -query GCF_000379845.1_ASM37984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d0ea6a0-9bdc-4d5e-b3a6-ca5271715cda/dqc_reference/reference_markers.fasta -out GCF_000379845.1_ASM37984v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:28,258] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:28,261] [INFO] Selected 26 target genomes.
[2024-01-25 19:10:28,261] [INFO] Target genome list was writen to GCF_000379845.1_ASM37984v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:28,277] [INFO] Task started: fastANI
[2024-01-25 19:10:28,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d37560f-e2d6-4e54-8204-5c616726b2c1/GCF_000379845.1_ASM37984v1_genomic.fna.gz --refList GCF_000379845.1_ASM37984v1_genomic.fna/target_genomes.txt --output GCF_000379845.1_ASM37984v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:41,185] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:41,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d0ea6a0-9bdc-4d5e-b3a6-ca5271715cda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:41,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d0ea6a0-9bdc-4d5e-b3a6-ca5271715cda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:41,194] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:10:41,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:41,195] [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 boevrei	strain=DSM 14165	GCA_000379845.1	346665	346665	type	True	100.0	789	790	95	conclusive
Moraxella ovis	strain=NCTC11227	GCA_900453105.1	29433	29433	type	True	78.9575	109	790	95	below_threshold
Moraxella bovis	strain=CCUG 2133	GCA_002014975.1	476	476	type	True	78.8666	148	790	95	below_threshold
Moraxella bovoculi	strain=237	GCA_000696305.2	386891	386891	type	True	78.518	96	790	95	below_threshold
Moraxella lacunata	strain=NBRC 102154	GCA_001591245.1	477	477	suspected-type	True	78.1996	131	790	95	below_threshold
Moraxella lacunata	strain=CCUG 4441	GCA_002027545.1	477	477	suspected-type	True	77.9204	146	790	95	below_threshold
Moraxella osloensis	strain=NCTC10465	GCA_900453115.1	34062	34062	suspected-type	True	77.7643	139	790	95	below_threshold
Moraxella osloensis	strain=FDAARGOS_870	GCA_016028755.1	34062	34062	suspected-type	True	77.7248	138	790	95	below_threshold
Moraxella osloensis	strain=CCUG 350	GCA_001679175.1	34062	34062	suspected-type	True	77.7185	135	790	95	below_threshold
Moraxella osloensis	strain=CCUG 350	GCA_001553955.1	34062	34062	suspected-type	True	77.634	140	790	95	below_threshold
Moraxella lincolnii	strain=CCUG 9405	GCA_002014765.1	90241	90241	type	True	76.9525	105	790	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	76.6253	55	790	95	below_threshold
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	75.7609	50	790	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:41,196] [INFO] DFAST Taxonomy check result was written to GCF_000379845.1_ASM37984v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:41,197] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:41,197] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:41,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d0ea6a0-9bdc-4d5e-b3a6-ca5271715cda/dqc_reference/checkm_data
[2024-01-25 19:10:41,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:41,222] [INFO] Task started: CheckM
[2024-01-25 19:10:41,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000379845.1_ASM37984v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000379845.1_ASM37984v1_genomic.fna/checkm_input GCF_000379845.1_ASM37984v1_genomic.fna/checkm_result
[2024-01-25 19:11:02,221] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:02,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:02,239] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:02,240] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:02,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000379845.1_ASM37984v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:02,240] [INFO] Task started: Blastn
[2024-01-25 19:11:02,240] [INFO] Running command: blastn -query GCF_000379845.1_ASM37984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d0ea6a0-9bdc-4d5e-b3a6-ca5271715cda/dqc_reference/reference_markers_gtdb.fasta -out GCF_000379845.1_ASM37984v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:03,244] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:03,248] [INFO] Selected 26 target genomes.
[2024-01-25 19:11:03,248] [INFO] Target genome list was writen to GCF_000379845.1_ASM37984v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:03,298] [INFO] Task started: fastANI
[2024-01-25 19:11:03,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d37560f-e2d6-4e54-8204-5c616726b2c1/GCF_000379845.1_ASM37984v1_genomic.fna.gz --refList GCF_000379845.1_ASM37984v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000379845.1_ASM37984v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:14,552] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:14,563] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:14,563] [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_000379845.1	s__Moraxella_A boevrei	100.0	789	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000320365.1	s__Moraxella_A macacae	80.6618	481	790	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_002027555.1	s__Moraxella equi	79.0341	137	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002014975.1	s__Moraxella bovis	78.8382	149	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	98.79	98.38	0.94	0.91	3	-
GCF_900453205.1	s__Moraxella lacunata_B	78.7592	155	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002027545.1	s__Moraxella lacunata	77.8991	147	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.28	95.16	0.88	0.84	9	-
GCF_009867135.1	s__Moraxella_A sp002478835	77.728	151	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0237	96.28	95.11	0.93	0.88	7	-
GCF_001553955.1	s__Moraxella_A osloensis	77.6561	139	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0237	96.88	95.23	0.89	0.83	12	-
GCA_014647715.1	s__Moraxella_A cinereus	77.5528	135	790	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_001656295.1	s__Moraxella catarrhalis_C	77.3543	79	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.44	97.90	0.94	0.92	5	-
GCF_001632285.1	s__Moraxella catarrhalis	77.2895	76	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.72	95.96	0.96	0.91	200	-
GCF_904846175.1	s__Psychrobacter immobilis_E	76.6021	55	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846345.1	s__Psychrobacter maritimus	76.4933	54	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.41	96.16	0.91	0.90	6	-
GCF_014861365.1	s__Psychrobacter sp014861365	76.3673	56	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.77	98.77	0.85	0.85	2	-
GCF_013414195.1	s__Psychrobacter sp013414195	76.2803	52	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001411745.2	s__Psychrobacter glacincola_A	76.1268	51	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	N/A	N/A	N/A	N/A	1	-
GCF_900101915.1	s__Psychrobacter pacificensis	75.7609	50	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	98.35	97.54	0.93	0.90	8	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:14,564] [INFO] GTDB search result was written to GCF_000379845.1_ASM37984v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:14,565] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:14,569] [INFO] DFAST_QC result json was written to GCF_000379845.1_ASM37984v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:14,569] [INFO] DFAST_QC completed!
[2024-01-25 19:11:14,569] [INFO] Total running time: 0h0m54s