[2024-01-24 13:18:41,137] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,139] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,139] [INFO] DQC Reference Directory: /var/lib/cwl/stgccf23efe-7f53-4ce7-b6cf-26b40003afeb/dqc_reference
[2024-01-24 13:18:42,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,388] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,388] [INFO] Running command: gunzip -c /var/lib/cwl/stg97ac23a1-5726-4b39-bfce-874966ddb6e3/GCF_022359095.1_ASM2235909v1_genomic.fna.gz | prodigal -d GCF_022359095.1_ASM2235909v1_genomic.fna/cds.fna -a GCF_022359095.1_ASM2235909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:49,521] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:49,522] [INFO] Task started: HMMsearch
[2024-01-24 13:18:49,522] [INFO] Running command: hmmsearch --tblout GCF_022359095.1_ASM2235909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccf23efe-7f53-4ce7-b6cf-26b40003afeb/dqc_reference/reference_markers.hmm GCF_022359095.1_ASM2235909v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:49,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:49,765] [INFO] Found 6/6 markers.
[2024-01-24 13:18:49,796] [INFO] Query marker FASTA was written to GCF_022359095.1_ASM2235909v1_genomic.fna/markers.fasta
[2024-01-24 13:18:49,796] [INFO] Task started: Blastn
[2024-01-24 13:18:49,796] [INFO] Running command: blastn -query GCF_022359095.1_ASM2235909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccf23efe-7f53-4ce7-b6cf-26b40003afeb/dqc_reference/reference_markers.fasta -out GCF_022359095.1_ASM2235909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:50,472] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:50,476] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:50,477] [INFO] Target genome list was writen to GCF_022359095.1_ASM2235909v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:50,501] [INFO] Task started: fastANI
[2024-01-24 13:18:50,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg97ac23a1-5726-4b39-bfce-874966ddb6e3/GCF_022359095.1_ASM2235909v1_genomic.fna.gz --refList GCF_022359095.1_ASM2235909v1_genomic.fna/target_genomes.txt --output GCF_022359095.1_ASM2235909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:57,718] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:57,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccf23efe-7f53-4ce7-b6cf-26b40003afeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:57,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccf23efe-7f53-4ce7-b6cf-26b40003afeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:57,734] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:18:57,734] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:57,734] [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 osloensis	strain=FDAARGOS_870	GCA_016028755.1	34062	34062	suspected-type	True	95.0825	754	906	95	conclusive
Moraxella osloensis	strain=CCUG 350	GCA_001679175.1	34062	34062	suspected-type	True	95.0501	740	906	95	conclusive
Moraxella osloensis	strain=CCUG 350	GCA_001553955.1	34062	34062	suspected-type	True	95.0263	771	906	95	conclusive
Moraxella osloensis	strain=NCTC10465	GCA_900453115.1	34062	34062	suspected-type	True	95.0143	767	906	95	conclusive
Moraxella nasovis	strain=ZY201115	GCA_022701215.1	2904121	2904121	type	True	78.6925	56	906	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	77.8591	99	906	95	below_threshold
Moraxella boevrei	strain=DSM 14165	GCA_000379845.1	346665	346665	type	True	77.7753	146	906	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	77.1016	93	906	95	below_threshold
Moraxella pluranimalium	strain=CCUG 54913	GCA_002014825.1	470453	470453	type	True	76.7745	88	906	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	76.5952	112	906	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	76.1176	90	906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:57,736] [INFO] DFAST Taxonomy check result was written to GCF_022359095.1_ASM2235909v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:57,736] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:57,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:57,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccf23efe-7f53-4ce7-b6cf-26b40003afeb/dqc_reference/checkm_data
[2024-01-24 13:18:57,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:57,766] [INFO] Task started: CheckM
[2024-01-24 13:18:57,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022359095.1_ASM2235909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022359095.1_ASM2235909v1_genomic.fna/checkm_input GCF_022359095.1_ASM2235909v1_genomic.fna/checkm_result
[2024-01-24 13:19:25,157] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:25,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,176] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:25,176] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:25,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022359095.1_ASM2235909v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:25,177] [INFO] Task started: Blastn
[2024-01-24 13:19:25,177] [INFO] Running command: blastn -query GCF_022359095.1_ASM2235909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccf23efe-7f53-4ce7-b6cf-26b40003afeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_022359095.1_ASM2235909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:26,271] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:26,275] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:26,275] [INFO] Target genome list was writen to GCF_022359095.1_ASM2235909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:26,394] [INFO] Task started: fastANI
[2024-01-24 13:19:26,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg97ac23a1-5726-4b39-bfce-874966ddb6e3/GCF_022359095.1_ASM2235909v1_genomic.fna.gz --refList GCF_022359095.1_ASM2235909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022359095.1_ASM2235909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:34,056] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:34,071] [INFO] Found 16 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:19:34,072] [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
GCA_014647715.1	s__Moraxella_A cinereus	95.6967	757	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0	95.56	95.32	0.87	0.85	40	inconclusive
GCF_001553955.1	s__Moraxella_A osloensis	95.0331	770	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0237	96.88	95.23	0.89	0.83	12	inconclusive
GCF_009867135.1	s__Moraxella_A sp002478835	94.8748	758	906	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_904846315.1	s__Psychrobacter jeotgali	78.4116	73	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000320365.1	s__Moraxella_A macacae	77.9204	103	906	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_000379845.1	s__Moraxella_A boevrei	77.8061	146	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377905.1	s__Psychrobacter sp002377905	77.7628	108	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012305.1	s__Psychrobacter arcticus	77.6383	96	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012847335.1	s__Psychrobacter sp012847335	77.3569	86	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.15	96.31	0.98	0.95	3	-
GCF_001921745.1	s__Psychrobacter sp001921745	77.128	72	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.15	99.15	0.97	0.97	2	-
GCF_002014855.1	s__Moraxella porci	76.8268	79	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.21	96.21	0.92	0.92	2	-
GCF_002014825.1	s__Moraxella pluranimalium	76.7745	88	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725675.1	s__Psychrobacter sanguinis_A	76.731	73	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.56	98.43	0.91	0.90	4	-
GCF_016464015.1	s__Psychrobacter sp016464015	76.7256	99	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016107545.1	s__Psychrobacter namhaensis	76.4078	86	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.25	97.66	0.93	0.91	5	-
GCF_904846225.1	s__Psychrobacter immobilis_F	76.272	82	906	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 13:19:34,074] [INFO] GTDB search result was written to GCF_022359095.1_ASM2235909v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:34,075] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:34,080] [INFO] DFAST_QC result json was written to GCF_022359095.1_ASM2235909v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:34,081] [INFO] DFAST_QC completed!
[2024-01-24 13:19:34,081] [INFO] Total running time: 0h0m53s