[2023-06-28 16:22:01,229] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:22:01,232] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:22:01,232] [INFO] DQC Reference Directory: /var/lib/cwl/stgea8c4fd2-9d67-4b96-b220-565df3153e74/dqc_reference
[2023-06-28 16:22:02,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:22:02,388] [INFO] Task started: Prodigal
[2023-06-28 16:22:02,388] [INFO] Running command: gunzip -c /var/lib/cwl/stg2365bddb-e1d5-4ab8-a373-444090429fa9/GCA_027397165.1_ASM2739716v1_genomic.fna.gz | prodigal -d GCA_027397165.1_ASM2739716v1_genomic.fna/cds.fna -a GCA_027397165.1_ASM2739716v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:22:09,101] [INFO] Task succeeded: Prodigal
[2023-06-28 16:22:09,101] [INFO] Task started: HMMsearch
[2023-06-28 16:22:09,101] [INFO] Running command: hmmsearch --tblout GCA_027397165.1_ASM2739716v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea8c4fd2-9d67-4b96-b220-565df3153e74/dqc_reference/reference_markers.hmm GCA_027397165.1_ASM2739716v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:22:09,286] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:22:09,288] [INFO] Found 6/6 markers.
[2023-06-28 16:22:09,317] [INFO] Query marker FASTA was written to GCA_027397165.1_ASM2739716v1_genomic.fna/markers.fasta
[2023-06-28 16:22:09,317] [INFO] Task started: Blastn
[2023-06-28 16:22:09,317] [INFO] Running command: blastn -query GCA_027397165.1_ASM2739716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea8c4fd2-9d67-4b96-b220-565df3153e74/dqc_reference/reference_markers.fasta -out GCA_027397165.1_ASM2739716v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:22:10,046] [INFO] Task succeeded: Blastn
[2023-06-28 16:22:10,050] [INFO] Selected 25 target genomes.
[2023-06-28 16:22:10,050] [INFO] Target genome list was writen to GCA_027397165.1_ASM2739716v1_genomic.fna/target_genomes.txt
[2023-06-28 16:22:10,052] [INFO] Task started: fastANI
[2023-06-28 16:22:10,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg2365bddb-e1d5-4ab8-a373-444090429fa9/GCA_027397165.1_ASM2739716v1_genomic.fna.gz --refList GCA_027397165.1_ASM2739716v1_genomic.fna/target_genomes.txt --output GCA_027397165.1_ASM2739716v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:22:27,752] [INFO] Task succeeded: fastANI
[2023-06-28 16:22:27,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea8c4fd2-9d67-4b96-b220-565df3153e74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:22:27,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea8c4fd2-9d67-4b96-b220-565df3153e74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:22:27,769] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:22:27,769] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:22:27,769] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.6476	238	813	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.3159	222	813	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.2157	160	813	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.7405	194	813	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.6958	151	813	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	75.4467	146	813	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	75.4442	147	813	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	75.3487	182	813	95	below_threshold
Nocardioides seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	75.3117	120	813	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	75.3116	143	813	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	75.2933	147	813	95	below_threshold
Nocardioides stalactiti	strain=1.0914	GCA_014180715.1	2755356	2755356	type	True	75.2643	146	813	95	below_threshold
Streptomyces lycii	strain=TRM 66187	GCA_009735685.1	2654337	2654337	type	True	75.2328	168	813	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	75.197	194	813	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	75.144	138	813	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	75.1049	198	813	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	75.0769	166	813	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	75.0743	181	813	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	75.0565	92	813	95	below_threshold
Actinoplanes lutulentus	strain=DSM 45883	GCA_014191235.1	1287878	1287878	type	True	75.0052	156	813	95	below_threshold
Mycolicibacterium agri	strain=JCM 6377	GCA_010722915.1	36811	36811	type	True	74.9619	100	813	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:22:27,772] [INFO] DFAST Taxonomy check result was written to GCA_027397165.1_ASM2739716v1_genomic.fna/tc_result.tsv
[2023-06-28 16:22:27,774] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:22:27,774] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:22:27,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea8c4fd2-9d67-4b96-b220-565df3153e74/dqc_reference/checkm_data
[2023-06-28 16:22:27,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:22:27,805] [INFO] Task started: CheckM
[2023-06-28 16:22:27,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027397165.1_ASM2739716v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027397165.1_ASM2739716v1_genomic.fna/checkm_input GCA_027397165.1_ASM2739716v1_genomic.fna/checkm_result
[2023-06-28 16:23:03,434] [INFO] Task succeeded: CheckM
[2023-06-28 16:23:03,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 16:23:03,456] [INFO] ===== Completeness check finished =====
[2023-06-28 16:23:03,456] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:23:03,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027397165.1_ASM2739716v1_genomic.fna/markers.fasta)
[2023-06-28 16:23:03,457] [INFO] Task started: Blastn
[2023-06-28 16:23:03,457] [INFO] Running command: blastn -query GCA_027397165.1_ASM2739716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea8c4fd2-9d67-4b96-b220-565df3153e74/dqc_reference/reference_markers_gtdb.fasta -out GCA_027397165.1_ASM2739716v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:23:04,543] [INFO] Task succeeded: Blastn
[2023-06-28 16:23:04,547] [INFO] Selected 17 target genomes.
[2023-06-28 16:23:04,548] [INFO] Target genome list was writen to GCA_027397165.1_ASM2739716v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:23:04,548] [INFO] Task started: fastANI
[2023-06-28 16:23:04,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg2365bddb-e1d5-4ab8-a373-444090429fa9/GCA_027397165.1_ASM2739716v1_genomic.fna.gz --refList GCA_027397165.1_ASM2739716v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027397165.1_ASM2739716v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:23:13,931] [INFO] Task succeeded: fastANI
[2023-06-28 16:23:13,946] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:23:13,946] [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_017883065.1	s__Bog-756 sp017883065	78.4103	290	813	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	-
GCA_003138855.1	s__Bog-756 sp003138855	78.3667	297	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.82	99.61	0.95	0.93	14	-
GCA_003164095.1	s__Bog-756 sp003164095	78.2714	328	813	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	-
GCA_003153575.1	s__Bog-756 sp003153575	78.2576	294	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.41	99.41	0.75	0.75	2	-
GCA_017883025.1	s__Bog-756 sp017883025	78.0569	246	813	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	-
GCA_015478655.1	s__Bog-756 sp015478655	77.956	254	813	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	-
GCA_903906055.1	s__Bog-756 sp903906055	77.7439	196	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.06	98.82	0.85	0.81	8	-
GCA_903849265.1	s__Bog-756 sp903849265	77.578	192	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	97.45	97.45	0.70	0.70	2	-
GCA_903894295.1	s__Bog-756 sp903894295	77.457	206	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.67	99.55	0.93	0.92	5	-
GCA_003157945.1	s__Bog-756 sp003157945	77.3757	187	813	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	-
GCA_017882995.1	s__Chersky-840 sp017882995	77.3091	182	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__Chersky-840	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003169235.1	s__Bog-473 sp003169235	77.1491	196	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-473	95.0	99.17	99.17	0.82	0.82	2	-
GCA_003151955.1	s__PALSA-743 sp003151955	77.0473	269	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__PALSA-743	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255565.1	s__RAAP-2 sp002255565	76.9383	159	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903860745.1	s__RAAP-2 sp903860745	76.8553	120	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.88	99.81	0.92	0.91	5	-
GCA_902805555.1	s__CADCSY01 sp902805555	76.5031	183	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__CADCSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377505.1	s__WHTX01 sp009377505	75.8887	221	813	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CAIXPF01;g__WHTX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:23:13,949] [INFO] GTDB search result was written to GCA_027397165.1_ASM2739716v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:23:13,950] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:23:13,954] [INFO] DFAST_QC result json was written to GCA_027397165.1_ASM2739716v1_genomic.fna/dqc_result.json
[2023-06-28 16:23:13,954] [INFO] DFAST_QC completed!
[2023-06-28 16:23:13,954] [INFO] Total running time: 0h1m13s