[2023-06-17 03:41:47,829] [INFO] DFAST_QC pipeline started.
[2023-06-17 03:41:47,834] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 03:41:47,834] [INFO] DQC Reference Directory: /var/lib/cwl/stgec505168-0998-4f47-b7c2-99522b45f146/dqc_reference
[2023-06-17 03:41:49,391] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 03:41:49,392] [INFO] Task started: Prodigal
[2023-06-17 03:41:49,393] [INFO] Running command: gunzip -c /var/lib/cwl/stge4e46dd7-51a5-42af-8abc-8c150f3fecca/GCA_013811665.1_ASM1381166v1_genomic.fna.gz | prodigal -d GCA_013811665.1_ASM1381166v1_genomic.fna/cds.fna -a GCA_013811665.1_ASM1381166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 03:41:55,489] [INFO] Task succeeded: Prodigal
[2023-06-17 03:41:55,489] [INFO] Task started: HMMsearch
[2023-06-17 03:41:55,489] [INFO] Running command: hmmsearch --tblout GCA_013811665.1_ASM1381166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec505168-0998-4f47-b7c2-99522b45f146/dqc_reference/reference_markers.hmm GCA_013811665.1_ASM1381166v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 03:41:55,664] [INFO] Task succeeded: HMMsearch
[2023-06-17 03:41:55,665] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge4e46dd7-51a5-42af-8abc-8c150f3fecca/GCA_013811665.1_ASM1381166v1_genomic.fna.gz]
[2023-06-17 03:41:55,692] [INFO] Query marker FASTA was written to GCA_013811665.1_ASM1381166v1_genomic.fna/markers.fasta
[2023-06-17 03:41:55,692] [INFO] Task started: Blastn
[2023-06-17 03:41:55,692] [INFO] Running command: blastn -query GCA_013811665.1_ASM1381166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec505168-0998-4f47-b7c2-99522b45f146/dqc_reference/reference_markers.fasta -out GCA_013811665.1_ASM1381166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:41:56,281] [INFO] Task succeeded: Blastn
[2023-06-17 03:41:56,284] [INFO] Selected 19 target genomes.
[2023-06-17 03:41:56,285] [INFO] Target genome list was writen to GCA_013811665.1_ASM1381166v1_genomic.fna/target_genomes.txt
[2023-06-17 03:41:56,288] [INFO] Task started: fastANI
[2023-06-17 03:41:56,288] [INFO] Running command: fastANI --query /var/lib/cwl/stge4e46dd7-51a5-42af-8abc-8c150f3fecca/GCA_013811665.1_ASM1381166v1_genomic.fna.gz --refList GCA_013811665.1_ASM1381166v1_genomic.fna/target_genomes.txt --output GCA_013811665.1_ASM1381166v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 03:42:11,772] [INFO] Task succeeded: fastANI
[2023-06-17 03:42:11,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec505168-0998-4f47-b7c2-99522b45f146/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 03:42:11,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec505168-0998-4f47-b7c2-99522b45f146/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 03:42:11,785] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 03:42:11,785] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 03:42:11,785] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.6969	127	432	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.1986	126	432	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.9006	95	432	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.1567	91	432	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.1377	74	432	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.7628	50	432	95	below_threshold
Micromonospora peucetia	strain=DSM 43363	GCA_900091625.1	47871	47871	type	True	75.3817	55	432	95	below_threshold
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	75.2684	52	432	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	75.2479	57	432	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	75.1821	72	432	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	75.1337	52	432	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	75.1025	56	432	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	74.9027	68	432	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	74.8217	53	432	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 03:42:11,787] [INFO] DFAST Taxonomy check result was written to GCA_013811665.1_ASM1381166v1_genomic.fna/tc_result.tsv
[2023-06-17 03:42:11,788] [INFO] ===== Taxonomy check completed =====
[2023-06-17 03:42:11,788] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 03:42:11,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec505168-0998-4f47-b7c2-99522b45f146/dqc_reference/checkm_data
[2023-06-17 03:42:11,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 03:42:11,817] [INFO] Task started: CheckM
[2023-06-17 03:42:11,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013811665.1_ASM1381166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013811665.1_ASM1381166v1_genomic.fna/checkm_input GCA_013811665.1_ASM1381166v1_genomic.fna/checkm_result
[2023-06-17 03:42:34,202] [INFO] Task succeeded: CheckM
[2023-06-17 03:42:34,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.15%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 03:42:34,218] [INFO] ===== Completeness check finished =====
[2023-06-17 03:42:34,218] [INFO] ===== Start GTDB Search =====
[2023-06-17 03:42:34,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013811665.1_ASM1381166v1_genomic.fna/markers.fasta)
[2023-06-17 03:42:34,219] [INFO] Task started: Blastn
[2023-06-17 03:42:34,219] [INFO] Running command: blastn -query GCA_013811665.1_ASM1381166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec505168-0998-4f47-b7c2-99522b45f146/dqc_reference/reference_markers_gtdb.fasta -out GCA_013811665.1_ASM1381166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:42:34,875] [INFO] Task succeeded: Blastn
[2023-06-17 03:42:34,879] [INFO] Selected 15 target genomes.
[2023-06-17 03:42:34,879] [INFO] Target genome list was writen to GCA_013811665.1_ASM1381166v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 03:42:34,894] [INFO] Task started: fastANI
[2023-06-17 03:42:34,894] [INFO] Running command: fastANI --query /var/lib/cwl/stge4e46dd7-51a5-42af-8abc-8c150f3fecca/GCA_013811665.1_ASM1381166v1_genomic.fna.gz --refList GCA_013811665.1_ASM1381166v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013811665.1_ASM1381166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 03:42:42,899] [INFO] Task succeeded: fastANI
[2023-06-17 03:42:42,911] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 03:42:42,911] [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_019048865.1	s__Aquihabitans sp019048865	81.7436	318	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513855.1	s__JAAZBK01 sp012513855	79.1968	174	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAZBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702505.1	s__JAAZBK01 sp016702505	78.1284	168	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAZBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	77.892	122	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882935.1	s__JADGOP01 sp017882935	77.5057	112	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JADGOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	77.2816	125	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	77.1709	133	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903953195.1	s__SXMI01 sp903953195	77.0297	57	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	98.58	98.55	0.81	0.80	3	-
GCF_014805525.1	s__Rhabdothermincola sediminis	76.9251	94	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__Rhabdothermincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805655.1	s__CADCTF01 sp902805655	76.8014	76	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCTF01;g__CADCTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.6861	100	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_004366205.1	s__SIRW01 sp004366205	76.6633	118	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921205.1	s__CAIXPF01 sp903921205	76.5815	87	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CAIXPF01;g__CAIXPF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883025.1	s__Bog-756 sp017883025	75.8578	55	432	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 03:42:42,913] [INFO] GTDB search result was written to GCA_013811665.1_ASM1381166v1_genomic.fna/result_gtdb.tsv
[2023-06-17 03:42:42,914] [INFO] ===== GTDB Search completed =====
[2023-06-17 03:42:42,918] [INFO] DFAST_QC result json was written to GCA_013811665.1_ASM1381166v1_genomic.fna/dqc_result.json
[2023-06-17 03:42:42,918] [INFO] DFAST_QC completed!
[2023-06-17 03:42:42,918] [INFO] Total running time: 0h0m55s