[2023-06-29 02:29:03,249] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:29:03,252] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:29:03,252] [INFO] DQC Reference Directory: /var/lib/cwl/stged8e7e0d-b645-46d0-827f-254ddb15f8fe/dqc_reference
[2023-06-29 02:29:05,806] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:29:05,807] [INFO] Task started: Prodigal
[2023-06-29 02:29:05,807] [INFO] Running command: gunzip -c /var/lib/cwl/stg16f38efc-f932-4df1-ba17-4a510080a5d4/GCA_005779205.1_ASM577920v1_genomic.fna.gz | prodigal -d GCA_005779205.1_ASM577920v1_genomic.fna/cds.fna -a GCA_005779205.1_ASM577920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:29:14,666] [INFO] Task succeeded: Prodigal
[2023-06-29 02:29:14,666] [INFO] Task started: HMMsearch
[2023-06-29 02:29:14,666] [INFO] Running command: hmmsearch --tblout GCA_005779205.1_ASM577920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged8e7e0d-b645-46d0-827f-254ddb15f8fe/dqc_reference/reference_markers.hmm GCA_005779205.1_ASM577920v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:29:14,925] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:29:14,926] [INFO] Found 6/6 markers.
[2023-06-29 02:29:14,959] [INFO] Query marker FASTA was written to GCA_005779205.1_ASM577920v1_genomic.fna/markers.fasta
[2023-06-29 02:29:14,960] [INFO] Task started: Blastn
[2023-06-29 02:29:14,960] [INFO] Running command: blastn -query GCA_005779205.1_ASM577920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged8e7e0d-b645-46d0-827f-254ddb15f8fe/dqc_reference/reference_markers.fasta -out GCA_005779205.1_ASM577920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:29:15,550] [INFO] Task succeeded: Blastn
[2023-06-29 02:29:15,555] [INFO] Selected 37 target genomes.
[2023-06-29 02:29:15,556] [INFO] Target genome list was writen to GCA_005779205.1_ASM577920v1_genomic.fna/target_genomes.txt
[2023-06-29 02:29:15,559] [INFO] Task started: fastANI
[2023-06-29 02:29:15,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg16f38efc-f932-4df1-ba17-4a510080a5d4/GCA_005779205.1_ASM577920v1_genomic.fna.gz --refList GCA_005779205.1_ASM577920v1_genomic.fna/target_genomes.txt --output GCA_005779205.1_ASM577920v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:29:44,176] [INFO] Task succeeded: fastANI
[2023-06-29 02:29:44,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged8e7e0d-b645-46d0-827f-254ddb15f8fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:29:44,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged8e7e0d-b645-46d0-827f-254ddb15f8fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:29:44,187] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:29:44,187] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 02:29:44,187] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.7719	124	955	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	74.8155	51	955	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	74.8155	51	955	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	74.6756	56	955	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 02:29:44,189] [INFO] DFAST Taxonomy check result was written to GCA_005779205.1_ASM577920v1_genomic.fna/tc_result.tsv
[2023-06-29 02:29:44,190] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:29:44,190] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:29:44,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged8e7e0d-b645-46d0-827f-254ddb15f8fe/dqc_reference/checkm_data
[2023-06-29 02:29:44,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:29:44,228] [INFO] Task started: CheckM
[2023-06-29 02:29:44,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005779205.1_ASM577920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005779205.1_ASM577920v1_genomic.fna/checkm_input GCA_005779205.1_ASM577920v1_genomic.fna/checkm_result
[2023-06-29 02:30:14,758] [INFO] Task succeeded: CheckM
[2023-06-29 02:30:14,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 2.60%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-29 02:30:14,785] [INFO] ===== Completeness check finished =====
[2023-06-29 02:30:14,786] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:30:14,786] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005779205.1_ASM577920v1_genomic.fna/markers.fasta)
[2023-06-29 02:30:14,786] [INFO] Task started: Blastn
[2023-06-29 02:30:14,787] [INFO] Running command: blastn -query GCA_005779205.1_ASM577920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged8e7e0d-b645-46d0-827f-254ddb15f8fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_005779205.1_ASM577920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:30:15,598] [INFO] Task succeeded: Blastn
[2023-06-29 02:30:15,603] [INFO] Selected 24 target genomes.
[2023-06-29 02:30:15,603] [INFO] Target genome list was writen to GCA_005779205.1_ASM577920v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:30:15,615] [INFO] Task started: fastANI
[2023-06-29 02:30:15,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg16f38efc-f932-4df1-ba17-4a510080a5d4/GCA_005779205.1_ASM577920v1_genomic.fna.gz --refList GCA_005779205.1_ASM577920v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005779205.1_ASM577920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:30:32,592] [INFO] Task succeeded: fastANI
[2023-06-29 02:30:32,616] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 02:30:32,617] [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_002737365.1	s__12-FULL-67-14b sp002737365	96.5846	770	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	97.27	96.58	0.83	0.80	6	conclusive
GCA_009694735.1	s__12-FULL-67-14b sp009694735	82.5678	562	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768615.1	s__12-FULL-67-14b sp001768615	79.7458	548	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871275.1	s__12-FULL-67-14b sp016871275	79.1	476	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018000455.1	s__CADEFD01 sp018000455	77.4783	269	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789705.1	s__CADEFD01 sp016789705	77.3672	300	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826065.1	s__CADEFD01 sp902826065	77.1323	292	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871195.1	s__VFZN01 sp016871195	76.7991	203	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__VFZN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813075.1	s__JACCSI01 sp013813075	76.5095	112	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JACCSI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650245.1	s__JAENWD01 sp016650245	76.4208	121	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JAENWD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883165.1	s__JADGOC01 sp017883165	76.3947	130	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JADGOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362195.1	s__QHWT01 sp013362195	76.1874	98	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871255.1	s__VFZH01 sp016871255	76.071	110	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__VFZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016210845.1	s__Gp6-AA40 sp016210845	76.0481	128	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767195.1	s__Gp6-AA40 sp001767195	75.9991	127	955	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.78	99.78	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-29 02:30:32,619] [INFO] GTDB search result was written to GCA_005779205.1_ASM577920v1_genomic.fna/result_gtdb.tsv
[2023-06-29 02:30:32,620] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:30:32,623] [INFO] DFAST_QC result json was written to GCA_005779205.1_ASM577920v1_genomic.fna/dqc_result.json
[2023-06-29 02:30:32,624] [INFO] DFAST_QC completed!
[2023-06-29 02:30:32,624] [INFO] Total running time: 0h1m29s