[2023-07-01 02:57:01,016] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:57:01,035] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:57:01,035] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3f489b7-99ce-4eca-8f23-e8ca107b3f06/dqc_reference
[2023-07-01 02:57:02,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:57:02,250] [INFO] Task started: Prodigal
[2023-07-01 02:57:02,251] [INFO] Running command: gunzip -c /var/lib/cwl/stgd06d6dbb-15db-414c-8c21-7c880f8a4f34/GCA_016708365.1_ASM1670836v1_genomic.fna.gz | prodigal -d GCA_016708365.1_ASM1670836v1_genomic.fna/cds.fna -a GCA_016708365.1_ASM1670836v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:57:19,314] [INFO] Task succeeded: Prodigal
[2023-07-01 02:57:19,315] [INFO] Task started: HMMsearch
[2023-07-01 02:57:19,315] [INFO] Running command: hmmsearch --tblout GCA_016708365.1_ASM1670836v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3f489b7-99ce-4eca-8f23-e8ca107b3f06/dqc_reference/reference_markers.hmm GCA_016708365.1_ASM1670836v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:57:19,607] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:57:19,609] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd06d6dbb-15db-414c-8c21-7c880f8a4f34/GCA_016708365.1_ASM1670836v1_genomic.fna.gz]
[2023-07-01 02:57:19,672] [INFO] Query marker FASTA was written to GCA_016708365.1_ASM1670836v1_genomic.fna/markers.fasta
[2023-07-01 02:57:19,673] [INFO] Task started: Blastn
[2023-07-01 02:57:19,673] [INFO] Running command: blastn -query GCA_016708365.1_ASM1670836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3f489b7-99ce-4eca-8f23-e8ca107b3f06/dqc_reference/reference_markers.fasta -out GCA_016708365.1_ASM1670836v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:57:20,429] [INFO] Task succeeded: Blastn
[2023-07-01 02:57:20,434] [INFO] Selected 15 target genomes.
[2023-07-01 02:57:20,434] [INFO] Target genome list was writen to GCA_016708365.1_ASM1670836v1_genomic.fna/target_genomes.txt
[2023-07-01 02:57:20,436] [INFO] Task started: fastANI
[2023-07-01 02:57:20,436] [INFO] Running command: fastANI --query /var/lib/cwl/stgd06d6dbb-15db-414c-8c21-7c880f8a4f34/GCA_016708365.1_ASM1670836v1_genomic.fna.gz --refList GCA_016708365.1_ASM1670836v1_genomic.fna/target_genomes.txt --output GCA_016708365.1_ASM1670836v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:57:35,593] [INFO] Task succeeded: fastANI
[2023-07-01 02:57:35,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3f489b7-99ce-4eca-8f23-e8ca107b3f06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:57:35,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3f489b7-99ce-4eca-8f23-e8ca107b3f06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:57:35,612] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:57:35,612] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 02:57:35,612] [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
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	80.986	672	1713	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	80.9074	696	1713	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	80.7137	712	1713	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	80.7029	694	1713	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.8562	603	1713	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.5409	556	1713	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.4516	573	1713	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.4327	596	1713	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.2627	533	1713	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.2072	675	1713	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.1747	716	1713	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.8821	622	1713	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.7973	538	1713	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.778	586	1713	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	78.7298	435	1713	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:57:35,615] [INFO] DFAST Taxonomy check result was written to GCA_016708365.1_ASM1670836v1_genomic.fna/tc_result.tsv
[2023-07-01 02:57:35,615] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:57:35,616] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:57:35,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3f489b7-99ce-4eca-8f23-e8ca107b3f06/dqc_reference/checkm_data
[2023-07-01 02:57:35,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:57:35,665] [INFO] Task started: CheckM
[2023-07-01 02:57:35,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708365.1_ASM1670836v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708365.1_ASM1670836v1_genomic.fna/checkm_input GCA_016708365.1_ASM1670836v1_genomic.fna/checkm_result
[2023-07-01 02:59:00,309] [INFO] Task succeeded: CheckM
[2023-07-01 02:59:00,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 02:59:00,360] [INFO] ===== Completeness check finished =====
[2023-07-01 02:59:00,360] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:59:00,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708365.1_ASM1670836v1_genomic.fna/markers.fasta)
[2023-07-01 02:59:00,361] [INFO] Task started: Blastn
[2023-07-01 02:59:00,361] [INFO] Running command: blastn -query GCA_016708365.1_ASM1670836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3f489b7-99ce-4eca-8f23-e8ca107b3f06/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708365.1_ASM1670836v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:59:01,579] [INFO] Task succeeded: Blastn
[2023-07-01 02:59:01,584] [INFO] Selected 16 target genomes.
[2023-07-01 02:59:01,584] [INFO] Target genome list was writen to GCA_016708365.1_ASM1670836v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:59:01,616] [INFO] Task started: fastANI
[2023-07-01 02:59:01,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgd06d6dbb-15db-414c-8c21-7c880f8a4f34/GCA_016708365.1_ASM1670836v1_genomic.fna.gz --refList GCA_016708365.1_ASM1670836v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708365.1_ASM1670836v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:59:17,854] [INFO] Task succeeded: fastANI
[2023-07-01 02:59:17,873] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 02:59:17,873] [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_016707445.1	s__Rubrivivax sp016707445	99.1274	1564	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.23	99.17	0.94	0.91	3	conclusive
GCA_016719535.1	s__Rubrivivax sp016719535	83.7084	1060	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859905.1	s__Rubrivivax sp014859905	81.7001	524	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724995.1	s__Rubrivivax sp001724995	81.3846	747	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709385.1	s__Rubrivivax sp016709385	81.1166	795	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.31	99.15	0.91	0.88	11	-
GCA_017302505.1	s__Rubrivivax sp017302505	80.9787	630	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016515.1	s__Rubrivivax albus	80.94	782	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725505.1	s__Rubrivivax sp001725505	80.9175	625	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284255.1	s__Rubrivivax gelatinosus_A	80.7531	722	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	98.28	98.28	0.94	0.94	2	-
GCA_018240325.1	s__Rubrivivax sp018240325	80.7052	662	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302495.1	s__Rubrivivax sp017302495	80.6568	597	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971105.1	s__Rubrivivax sp018971105	80.3757	604	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241895.1	s__Rubrivivax sp018241895	80.3508	653	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790515.1	s__Aquabacterium_A sp016790515	80.3111	695	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702655.1	s__CAIKUF01 sp016702655	79.8375	711	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476815.1	s__Pseudacidovorax intermedius_A	78.639	547	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:59:17,876] [INFO] GTDB search result was written to GCA_016708365.1_ASM1670836v1_genomic.fna/result_gtdb.tsv
[2023-07-01 02:59:17,876] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:59:17,880] [INFO] DFAST_QC result json was written to GCA_016708365.1_ASM1670836v1_genomic.fna/dqc_result.json
[2023-07-01 02:59:17,880] [INFO] DFAST_QC completed!
[2023-07-01 02:59:17,880] [INFO] Total running time: 0h2m17s