[2024-01-24 13:32:42,431] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,433] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg6de440c7-8932-4ac0-bb23-18b7f58432c5/dqc_reference
[2024-01-24 13:32:43,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,705] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,706] [INFO] Running command: gunzip -c /var/lib/cwl/stg29aeb4e2-0f0c-4592-a42a-131c45d8503d/GCF_001636015.1_ASM163601v1_genomic.fna.gz | prodigal -d GCF_001636015.1_ASM163601v1_genomic.fna/cds.fna -a GCF_001636015.1_ASM163601v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:50,088] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:50,089] [INFO] Task started: HMMsearch
[2024-01-24 13:32:50,089] [INFO] Running command: hmmsearch --tblout GCF_001636015.1_ASM163601v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6de440c7-8932-4ac0-bb23-18b7f58432c5/dqc_reference/reference_markers.hmm GCF_001636015.1_ASM163601v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:50,281] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:50,283] [INFO] Found 6/6 markers.
[2024-01-24 13:32:50,309] [INFO] Query marker FASTA was written to GCF_001636015.1_ASM163601v1_genomic.fna/markers.fasta
[2024-01-24 13:32:50,309] [INFO] Task started: Blastn
[2024-01-24 13:32:50,310] [INFO] Running command: blastn -query GCF_001636015.1_ASM163601v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6de440c7-8932-4ac0-bb23-18b7f58432c5/dqc_reference/reference_markers.fasta -out GCF_001636015.1_ASM163601v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:50,954] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:50,956] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:50,957] [INFO] Target genome list was writen to GCF_001636015.1_ASM163601v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:50,963] [INFO] Task started: fastANI
[2024-01-24 13:32:50,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg29aeb4e2-0f0c-4592-a42a-131c45d8503d/GCF_001636015.1_ASM163601v1_genomic.fna.gz --refList GCF_001636015.1_ASM163601v1_genomic.fna/target_genomes.txt --output GCF_001636015.1_ASM163601v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:59,166] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:59,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6de440c7-8932-4ac0-bb23-18b7f58432c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:59,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6de440c7-8932-4ac0-bb23-18b7f58432c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:59,178] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:32:59,178] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:32:59,178] [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 ovis	strain=199/55	GCA_001636015.1	29433	29433	type	True	100.0	767	768	95	inconclusive
Moraxella ovis	strain=NCTC11227	GCA_900453105.1	29433	29433	type	True	99.9971	766	768	95	inconclusive
Moraxella bovoculi	strain=237	GCA_000696305.2	386891	386891	type	True	95.9597	608	768	95	inconclusive
Moraxella caprae	strain=NCTC12877	GCA_900453285.1	90240	90240	type	True	85.5597	291	768	95	below_threshold
Moraxella caprae	strain=DSM 19149	GCA_000426885.1	90240	90240	type	True	85.3268	285	768	95	below_threshold
Moraxella lacunata	strain=CCUG 4441	GCA_002027545.1	477	477	suspected-type	True	83.0469	281	768	95	below_threshold
Moraxella lacunata	strain=NBRC 102154	GCA_001591245.1	477	477	suspected-type	True	82.9639	251	768	95	below_threshold
Moraxella caviae	strain=NCTC10293	GCA_900453175.1	34060	34060	type	True	78.9516	272	768	95	below_threshold
Moraxella nasovis	strain=ZY201115	GCA_022701215.1	2904121	2904121	type	True	78.6541	199	768	95	below_threshold
Moraxella caviae	strain=CCUG 355	GCA_002014985.1	34060	34060	type	True	78.5453	248	768	95	below_threshold
Moraxella porci	strain=CCUG 54912	GCA_002014855.1	1288392	1288392	type	True	78.3248	196	768	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	76.666	54	768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:59,180] [INFO] DFAST Taxonomy check result was written to GCF_001636015.1_ASM163601v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:59,180] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:59,180] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:59,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6de440c7-8932-4ac0-bb23-18b7f58432c5/dqc_reference/checkm_data
[2024-01-24 13:32:59,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:59,207] [INFO] Task started: CheckM
[2024-01-24 13:32:59,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001636015.1_ASM163601v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001636015.1_ASM163601v1_genomic.fna/checkm_input GCF_001636015.1_ASM163601v1_genomic.fna/checkm_result
[2024-01-24 13:33:25,545] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:25,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:25,561] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:25,561] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:25,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001636015.1_ASM163601v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:25,562] [INFO] Task started: Blastn
[2024-01-24 13:33:25,562] [INFO] Running command: blastn -query GCF_001636015.1_ASM163601v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6de440c7-8932-4ac0-bb23-18b7f58432c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001636015.1_ASM163601v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:26,666] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:26,669] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:26,669] [INFO] Target genome list was writen to GCF_001636015.1_ASM163601v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:26,706] [INFO] Task started: fastANI
[2024-01-24 13:33:26,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg29aeb4e2-0f0c-4592-a42a-131c45d8503d/GCF_001636015.1_ASM163601v1_genomic.fna.gz --refList GCF_001636015.1_ASM163601v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001636015.1_ASM163601v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:33,855] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:33,865] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:33,866] [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_001636015.1	s__Moraxella ovis	100.0	766	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	97.95	96.93	0.90	0.85	8	conclusive
GCF_000696305.2	s__Moraxella bovoculi	95.9597	608	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	98.49	98.41	0.96	0.96	5	-
GCF_000426885.1	s__Moraxella caprae	85.3711	283	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	99.99	99.99	1.00	1.00	2	-
GCF_002014975.1	s__Moraxella bovis	84.8344	281	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	98.79	98.38	0.94	0.91	3	-
GCF_002027555.1	s__Moraxella equi	83.832	270	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900453205.1	s__Moraxella lacunata_B	83.7681	294	768	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	83.0988	279	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.28	95.16	0.88	0.84	9	-
GCF_001679005.1	s__Moraxella nonliquefaciens	80.0528	220	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.13	98.18	0.96	0.92	5	-
GCF_002014985.1	s__Moraxella caviae	78.5453	248	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.91	99.82	0.90	0.81	3	-
GCF_002014965.1	s__Moraxella canis	78.3572	164	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	97.14	96.86	0.93	0.92	4	-
GCF_002014855.1	s__Moraxella porci	78.3448	195	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.21	96.21	0.92	0.92	2	-
GCF_900156515.1	s__Moraxella cuniculi	78.2071	165	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.10	98.21	0.93	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:33,867] [INFO] GTDB search result was written to GCF_001636015.1_ASM163601v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:33,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:33,872] [INFO] DFAST_QC result json was written to GCF_001636015.1_ASM163601v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:33,872] [INFO] DFAST_QC completed!
[2024-01-24 13:33:33,872] [INFO] Total running time: 0h0m51s