[2024-01-24 12:44:50,452] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:50,454] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:50,454] [INFO] DQC Reference Directory: /var/lib/cwl/stgc13bf362-8c29-444f-b149-54544bc60ac7/dqc_reference
[2024-01-24 12:44:51,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:51,677] [INFO] Task started: Prodigal
[2024-01-24 12:44:51,677] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a795f27-8690-4b4f-a3e4-8110ed7d96c1/GCF_002014825.1_ASM201482v1_genomic.fna.gz | prodigal -d GCF_002014825.1_ASM201482v1_genomic.fna/cds.fna -a GCF_002014825.1_ASM201482v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:58,308] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:58,309] [INFO] Task started: HMMsearch
[2024-01-24 12:44:58,309] [INFO] Running command: hmmsearch --tblout GCF_002014825.1_ASM201482v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc13bf362-8c29-444f-b149-54544bc60ac7/dqc_reference/reference_markers.hmm GCF_002014825.1_ASM201482v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:58,550] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:58,552] [INFO] Found 6/6 markers.
[2024-01-24 12:44:58,574] [INFO] Query marker FASTA was written to GCF_002014825.1_ASM201482v1_genomic.fna/markers.fasta
[2024-01-24 12:44:58,575] [INFO] Task started: Blastn
[2024-01-24 12:44:58,575] [INFO] Running command: blastn -query GCF_002014825.1_ASM201482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc13bf362-8c29-444f-b149-54544bc60ac7/dqc_reference/reference_markers.fasta -out GCF_002014825.1_ASM201482v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:59,254] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:59,257] [INFO] Selected 20 target genomes.
[2024-01-24 12:44:59,258] [INFO] Target genome list was writen to GCF_002014825.1_ASM201482v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:59,317] [INFO] Task started: fastANI
[2024-01-24 12:44:59,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a795f27-8690-4b4f-a3e4-8110ed7d96c1/GCF_002014825.1_ASM201482v1_genomic.fna.gz --refList GCF_002014825.1_ASM201482v1_genomic.fna/target_genomes.txt --output GCF_002014825.1_ASM201482v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:08,340] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:08,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc13bf362-8c29-444f-b149-54544bc60ac7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:08,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc13bf362-8c29-444f-b149-54544bc60ac7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:08,356] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:08,356] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:08,356] [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 pluranimalium	strain=CCUG 54913	GCA_002014825.1	470453	470453	type	True	100.0	736	738	95	conclusive
Moraxella porci	strain=CCUG 54912	GCA_002014855.1	1288392	1288392	type	True	85.8744	485	738	95	below_threshold
Moraxella cuniculi	strain=CCUG 2154	GCA_002015175.1	34061	34061	type	True	78.9229	298	738	95	below_threshold
Moraxella cuniculi	strain=DSM 21768	GCA_900156515.1	34061	34061	type	True	78.921	295	738	95	below_threshold
Moraxella cuniculi	strain=NCTC10297	GCA_900637105.1	34061	34061	type	True	78.7845	307	738	95	below_threshold
Moraxella canis	strain=CCUG 8415A	GCA_002014965.1	90239	90239	type	True	78.5754	318	738	95	below_threshold
Moraxella catarrhalis	strain=CCUG 353	GCA_001632285.1	480	480	type	True	78.3692	218	738	95	below_threshold
Moraxella caviae	strain=NCTC10293	GCA_900453175.1	34060	34060	type	True	78.3499	267	738	95	below_threshold
Moraxella catarrhalis	strain=NCTC11020	GCA_900476075.1	480	480	type	True	78.2952	222	738	95	below_threshold
Moraxella caviae	strain=CCUG 355	GCA_002014985.1	34060	34060	type	True	78.2528	258	738	95	below_threshold
Moraxella nasovis	strain=ZY201115	GCA_022701215.1	2904121	2904121	type	True	77.9315	164	738	95	below_threshold
Moraxella oblonga	strain=NBRC 102422	GCA_001598275.1	200413	200413	type	True	76.9235	142	738	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:08,358] [INFO] DFAST Taxonomy check result was written to GCF_002014825.1_ASM201482v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:08,358] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:08,359] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:08,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc13bf362-8c29-444f-b149-54544bc60ac7/dqc_reference/checkm_data
[2024-01-24 12:45:08,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:08,385] [INFO] Task started: CheckM
[2024-01-24 12:45:08,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002014825.1_ASM201482v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002014825.1_ASM201482v1_genomic.fna/checkm_input GCF_002014825.1_ASM201482v1_genomic.fna/checkm_result
[2024-01-24 12:45:34,874] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:34,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:34,899] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:34,900] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:34,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002014825.1_ASM201482v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:34,900] [INFO] Task started: Blastn
[2024-01-24 12:45:34,901] [INFO] Running command: blastn -query GCF_002014825.1_ASM201482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc13bf362-8c29-444f-b149-54544bc60ac7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002014825.1_ASM201482v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:35,989] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:35,992] [INFO] Selected 13 target genomes.
[2024-01-24 12:45:35,992] [INFO] Target genome list was writen to GCF_002014825.1_ASM201482v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:36,010] [INFO] Task started: fastANI
[2024-01-24 12:45:36,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a795f27-8690-4b4f-a3e4-8110ed7d96c1/GCF_002014825.1_ASM201482v1_genomic.fna.gz --refList GCF_002014825.1_ASM201482v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002014825.1_ASM201482v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:41,997] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:42,013] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:42,013] [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_002014825.1	s__Moraxella pluranimalium	100.0	736	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002014855.1	s__Moraxella porci	85.9047	483	738	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	78.9297	293	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.10	98.21	0.93	0.87	3	-
GCF_001656295.1	s__Moraxella catarrhalis_C	78.6004	288	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.44	97.90	0.94	0.92	5	-
GCF_002014965.1	s__Moraxella canis	78.5627	319	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	97.14	96.86	0.93	0.92	4	-
GCF_001632285.1	s__Moraxella catarrhalis	78.3692	218	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.72	95.96	0.96	0.91	200	-
GCF_002014985.1	s__Moraxella caviae	78.217	261	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.91	99.82	0.90	0.81	3	-
GCF_002224245.2	s__Moraxella sp002224245	77.5978	163	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498085.1	s__Psychrobacter sp017498085	76.7263	67	738	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 12:45:42,015] [INFO] GTDB search result was written to GCF_002014825.1_ASM201482v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:42,016] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:42,020] [INFO] DFAST_QC result json was written to GCF_002014825.1_ASM201482v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:42,020] [INFO] DFAST_QC completed!
[2024-01-24 12:45:42,020] [INFO] Total running time: 0h0m52s