[2024-01-25 19:05:20,662] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:20,666] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:20,666] [INFO] DQC Reference Directory: /var/lib/cwl/stg89349298-3814-4c73-871a-db5bc75401a0/dqc_reference
[2024-01-25 19:05:21,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:21,813] [INFO] Task started: Prodigal
[2024-01-25 19:05:21,813] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5c99dee-6548-4acd-9fee-24285a664480/GCF_002014975.1_ASM201497v1_genomic.fna.gz | prodigal -d GCF_002014975.1_ASM201497v1_genomic.fna/cds.fna -a GCF_002014975.1_ASM201497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:28,460] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:28,460] [INFO] Task started: HMMsearch
[2024-01-25 19:05:28,460] [INFO] Running command: hmmsearch --tblout GCF_002014975.1_ASM201497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89349298-3814-4c73-871a-db5bc75401a0/dqc_reference/reference_markers.hmm GCF_002014975.1_ASM201497v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:28,659] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:28,660] [INFO] Found 6/6 markers.
[2024-01-25 19:05:28,687] [INFO] Query marker FASTA was written to GCF_002014975.1_ASM201497v1_genomic.fna/markers.fasta
[2024-01-25 19:05:28,687] [INFO] Task started: Blastn
[2024-01-25 19:05:28,687] [INFO] Running command: blastn -query GCF_002014975.1_ASM201497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89349298-3814-4c73-871a-db5bc75401a0/dqc_reference/reference_markers.fasta -out GCF_002014975.1_ASM201497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:29,299] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:29,302] [INFO] Selected 12 target genomes.
[2024-01-25 19:05:29,302] [INFO] Target genome list was writen to GCF_002014975.1_ASM201497v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:29,371] [INFO] Task started: fastANI
[2024-01-25 19:05:29,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c99dee-6548-4acd-9fee-24285a664480/GCF_002014975.1_ASM201497v1_genomic.fna.gz --refList GCF_002014975.1_ASM201497v1_genomic.fna/target_genomes.txt --output GCF_002014975.1_ASM201497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:37,750] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:37,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89349298-3814-4c73-871a-db5bc75401a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:37,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89349298-3814-4c73-871a-db5bc75401a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:37,756] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:05:37,757] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:05:37,757] [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 bovis	strain=CCUG 2133	GCA_002014975.1	476	476	type	True	100.0	860	866	95	inconclusive
Moraxella caprae	strain=DSM 19149	GCA_000426885.1	90240	90240	type	True	95.6695	677	866	95	inconclusive
Moraxella caprae	strain=NCTC12877	GCA_900453285.1	90240	90240	type	True	95.483	715	866	95	inconclusive
Moraxella equi	strain=CCUG 4950	GCA_002027555.1	60442	60442	type	True	94.6566	652	866	95	below_threshold
Moraxella equi	strain=NCTC11012	GCA_900453335.1	60442	60442	type	True	94.3946	714	866	95	below_threshold
Moraxella bovoculi	strain=237	GCA_000696305.2	386891	386891	type	True	85.6387	259	866	95	below_threshold
Moraxella ovis	strain=NCTC11227	GCA_900453105.1	29433	29433	type	True	84.4569	285	866	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:37,758] [INFO] DFAST Taxonomy check result was written to GCF_002014975.1_ASM201497v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:37,760] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:37,760] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:37,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89349298-3814-4c73-871a-db5bc75401a0/dqc_reference/checkm_data
[2024-01-25 19:05:37,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:37,790] [INFO] Task started: CheckM
[2024-01-25 19:05:37,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002014975.1_ASM201497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002014975.1_ASM201497v1_genomic.fna/checkm_input GCF_002014975.1_ASM201497v1_genomic.fna/checkm_result
[2024-01-25 19:06:02,220] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:02,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:02,240] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:02,240] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:02,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002014975.1_ASM201497v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:02,240] [INFO] Task started: Blastn
[2024-01-25 19:06:02,240] [INFO] Running command: blastn -query GCF_002014975.1_ASM201497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89349298-3814-4c73-871a-db5bc75401a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002014975.1_ASM201497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:03,209] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:03,212] [INFO] Selected 8 target genomes.
[2024-01-25 19:06:03,212] [INFO] Target genome list was writen to GCF_002014975.1_ASM201497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:03,241] [INFO] Task started: fastANI
[2024-01-25 19:06:03,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c99dee-6548-4acd-9fee-24285a664480/GCF_002014975.1_ASM201497v1_genomic.fna.gz --refList GCF_002014975.1_ASM201497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002014975.1_ASM201497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:09,480] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:09,486] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 19:06:09,487] [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_002014975.1	s__Moraxella bovis	100.0	860	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	98.79	98.38	0.94	0.91	3	inconclusive
GCF_000426885.1	s__Moraxella caprae	95.6921	676	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	99.99	99.99	1.00	1.00	2	inconclusive
GCF_002027555.1	s__Moraxella equi	94.6566	652	866	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	94.2979	717	866	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	90.5162	645	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.28	95.16	0.88	0.84	9	-
GCF_000696305.2	s__Moraxella bovoculi	85.6387	259	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	98.49	98.41	0.96	0.96	5	-
GCF_001636015.1	s__Moraxella ovis	84.645	284	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	97.95	96.93	0.90	0.85	8	-
GCF_001679005.1	s__Moraxella nonliquefaciens	83.8885	550	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.13	98.18	0.96	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:09,489] [INFO] GTDB search result was written to GCF_002014975.1_ASM201497v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:09,489] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:09,492] [INFO] DFAST_QC result json was written to GCF_002014975.1_ASM201497v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:09,492] [INFO] DFAST_QC completed!
[2024-01-25 19:06:09,492] [INFO] Total running time: 0h0m49s