[2024-01-24 15:10:40,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:40,806] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:40,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg32af4c92-3c36-41de-af17-5126c4d21557/dqc_reference
[2024-01-24 15:10:42,253] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,254] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,255] [INFO] Running command: gunzip -c /var/lib/cwl/stged778bc1-0221-43af-af9e-4d857bb3875b/GCF_001591245.1_ASM159124v1_genomic.fna.gz | prodigal -d GCF_001591245.1_ASM159124v1_genomic.fna/cds.fna -a GCF_001591245.1_ASM159124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:49,213] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:49,213] [INFO] Task started: HMMsearch
[2024-01-24 15:10:49,214] [INFO] Running command: hmmsearch --tblout GCF_001591245.1_ASM159124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32af4c92-3c36-41de-af17-5126c4d21557/dqc_reference/reference_markers.hmm GCF_001591245.1_ASM159124v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:49,472] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:49,473] [INFO] Found 6/6 markers.
[2024-01-24 15:10:49,498] [INFO] Query marker FASTA was written to GCF_001591245.1_ASM159124v1_genomic.fna/markers.fasta
[2024-01-24 15:10:49,498] [INFO] Task started: Blastn
[2024-01-24 15:10:49,499] [INFO] Running command: blastn -query GCF_001591245.1_ASM159124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32af4c92-3c36-41de-af17-5126c4d21557/dqc_reference/reference_markers.fasta -out GCF_001591245.1_ASM159124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:50,154] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:50,157] [INFO] Selected 15 target genomes.
[2024-01-24 15:10:50,157] [INFO] Target genome list was writen to GCF_001591245.1_ASM159124v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:50,178] [INFO] Task started: fastANI
[2024-01-24 15:10:50,179] [INFO] Running command: fastANI --query /var/lib/cwl/stged778bc1-0221-43af-af9e-4d857bb3875b/GCF_001591245.1_ASM159124v1_genomic.fna.gz --refList GCF_001591245.1_ASM159124v1_genomic.fna/target_genomes.txt --output GCF_001591245.1_ASM159124v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:59,978] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:59,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32af4c92-3c36-41de-af17-5126c4d21557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:59,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32af4c92-3c36-41de-af17-5126c4d21557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:59,989] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:10:59,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:59,989] [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 lacunata	strain=NBRC 102154	GCA_001591245.1	477	477	suspected-type	True	100.0	721	730	95	conclusive
Moraxella lacunata	strain=CCUG 4441	GCA_002027545.1	477	477	suspected-type	True	99.9968	727	730	95	conclusive
Moraxella caprae	strain=DSM 19149	GCA_000426885.1	90240	90240	type	True	90.5507	547	730	95	below_threshold
Moraxella caprae	strain=NCTC12877	GCA_900453285.1	90240	90240	type	True	90.4902	564	730	95	below_threshold
Moraxella bovis	strain=CCUG 2133	GCA_002014975.1	476	476	type	True	90.4259	565	730	95	below_threshold
Moraxella equi	strain=CCUG 4950	GCA_002027555.1	60442	60442	type	True	90.3641	551	730	95	below_threshold
Moraxella equi	strain=NCTC11012	GCA_900453335.1	60442	60442	type	True	90.3031	586	730	95	below_threshold
Moraxella nonliquefaciens	strain=CCUG 348	GCA_001679005.1	478	478	type	True	87.4424	505	730	95	below_threshold
Moraxella nonliquefaciens	strain=FDAARGOS_869	GCA_016028775.1	478	478	type	True	87.3025	520	730	95	below_threshold
Moraxella ovis	strain=NCTC11227	GCA_900453105.1	29433	29433	type	True	82.7982	241	730	95	below_threshold
Moraxella nasovis	strain=ZY201115	GCA_022701215.1	2904121	2904121	type	True	78.055	154	730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:59,991] [INFO] DFAST Taxonomy check result was written to GCF_001591245.1_ASM159124v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:59,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:59,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:59,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32af4c92-3c36-41de-af17-5126c4d21557/dqc_reference/checkm_data
[2024-01-24 15:10:59,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:00,029] [INFO] Task started: CheckM
[2024-01-24 15:11:00,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591245.1_ASM159124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591245.1_ASM159124v1_genomic.fna/checkm_input GCF_001591245.1_ASM159124v1_genomic.fna/checkm_result
[2024-01-24 15:11:27,770] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:27,771] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:27,790] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:27,790] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:27,791] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591245.1_ASM159124v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:27,791] [INFO] Task started: Blastn
[2024-01-24 15:11:27,791] [INFO] Running command: blastn -query GCF_001591245.1_ASM159124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32af4c92-3c36-41de-af17-5126c4d21557/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591245.1_ASM159124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:28,905] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:28,909] [INFO] Selected 7 target genomes.
[2024-01-24 15:11:28,909] [INFO] Target genome list was writen to GCF_001591245.1_ASM159124v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:28,914] [INFO] Task started: fastANI
[2024-01-24 15:11:28,914] [INFO] Running command: fastANI --query /var/lib/cwl/stged778bc1-0221-43af-af9e-4d857bb3875b/GCF_001591245.1_ASM159124v1_genomic.fna.gz --refList GCF_001591245.1_ASM159124v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591245.1_ASM159124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:33,498] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:33,510] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:33,510] [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_002027545.1	s__Moraxella lacunata	99.9968	727	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.28	95.16	0.88	0.84	9	conclusive
GCF_900453205.1	s__Moraxella lacunata_B	90.873	584	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426885.1	s__Moraxella caprae	90.5215	548	730	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	90.3975	566	730	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	90.3641	551	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001679005.1	s__Moraxella nonliquefaciens	87.4217	506	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.13	98.18	0.96	0.92	5	-
GCF_001636015.1	s__Moraxella ovis	82.8263	247	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	97.95	96.93	0.90	0.85	8	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:33,512] [INFO] GTDB search result was written to GCF_001591245.1_ASM159124v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:33,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:33,516] [INFO] DFAST_QC result json was written to GCF_001591245.1_ASM159124v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:33,516] [INFO] DFAST_QC completed!
[2024-01-24 15:11:33,516] [INFO] Total running time: 0h0m53s