[2023-06-28 22:48:24,602] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:48:24,604] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:48:24,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg69336af0-2eef-4771-ac09-395c39262a92/dqc_reference
[2023-06-28 22:48:25,846] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:48:25,847] [INFO] Task started: Prodigal
[2023-06-28 22:48:25,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg709d8fd2-ea51-4c15-aefe-866226c71549/GCA_027396995.1_ASM2739699v1_genomic.fna.gz | prodigal -d GCA_027396995.1_ASM2739699v1_genomic.fna/cds.fna -a GCA_027396995.1_ASM2739699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:48:33,496] [INFO] Task succeeded: Prodigal
[2023-06-28 22:48:33,497] [INFO] Task started: HMMsearch
[2023-06-28 22:48:33,497] [INFO] Running command: hmmsearch --tblout GCA_027396995.1_ASM2739699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69336af0-2eef-4771-ac09-395c39262a92/dqc_reference/reference_markers.hmm GCA_027396995.1_ASM2739699v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:48:33,725] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:48:33,727] [INFO] Found 6/6 markers.
[2023-06-28 22:48:33,756] [INFO] Query marker FASTA was written to GCA_027396995.1_ASM2739699v1_genomic.fna/markers.fasta
[2023-06-28 22:48:33,756] [INFO] Task started: Blastn
[2023-06-28 22:48:33,756] [INFO] Running command: blastn -query GCA_027396995.1_ASM2739699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69336af0-2eef-4771-ac09-395c39262a92/dqc_reference/reference_markers.fasta -out GCA_027396995.1_ASM2739699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:48:34,458] [INFO] Task succeeded: Blastn
[2023-06-28 22:48:34,462] [INFO] Selected 22 target genomes.
[2023-06-28 22:48:34,462] [INFO] Target genome list was writen to GCA_027396995.1_ASM2739699v1_genomic.fna/target_genomes.txt
[2023-06-28 22:48:34,464] [INFO] Task started: fastANI
[2023-06-28 22:48:34,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg709d8fd2-ea51-4c15-aefe-866226c71549/GCA_027396995.1_ASM2739699v1_genomic.fna.gz --refList GCA_027396995.1_ASM2739699v1_genomic.fna/target_genomes.txt --output GCA_027396995.1_ASM2739699v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:48:51,020] [INFO] Task succeeded: fastANI
[2023-06-28 22:48:51,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69336af0-2eef-4771-ac09-395c39262a92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:48:51,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69336af0-2eef-4771-ac09-395c39262a92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:48:51,037] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:48:51,037] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:48:51,037] [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 sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.8055	118	860	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.3678	181	860	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.2988	209	860	95	below_threshold
Acidimicrobium ferrooxidans	strain=DSM 10331	GCA_000023265.1	53635	53635	type	True	76.2311	65	860	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.5997	168	860	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.5208	140	860	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	75.4446	138	860	95	below_threshold
Micromonospora inyonensis	strain=DSM 46123	GCA_900091415.1	47866	47866	type	True	75.4022	127	860	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.3876	98	860	95	below_threshold
Actinoalloteichus hymeniacidonis	strain=DSM 45092	GCA_014203365.1	340345	340345	type	True	75.3573	60	860	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	75.3339	157	860	95	below_threshold
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	75.2932	108	860	95	below_threshold
Actinoalloteichus hymeniacidonis	strain=HPA177(T) (=DSM 45092(T))	GCA_001747425.1	340345	340345	type	True	75.2872	60	860	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	75.0464	127	860	95	below_threshold
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	74.7317	67	860	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	74.7	69	860	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:48:51,040] [INFO] DFAST Taxonomy check result was written to GCA_027396995.1_ASM2739699v1_genomic.fna/tc_result.tsv
[2023-06-28 22:48:51,041] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:48:51,041] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:48:51,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69336af0-2eef-4771-ac09-395c39262a92/dqc_reference/checkm_data
[2023-06-28 22:48:51,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:48:51,076] [INFO] Task started: CheckM
[2023-06-28 22:48:51,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027396995.1_ASM2739699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027396995.1_ASM2739699v1_genomic.fna/checkm_input GCA_027396995.1_ASM2739699v1_genomic.fna/checkm_result
[2023-06-28 22:49:18,930] [INFO] Task succeeded: CheckM
[2023-06-28 22:49:18,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:49:18,954] [INFO] ===== Completeness check finished =====
[2023-06-28 22:49:18,954] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:49:18,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027396995.1_ASM2739699v1_genomic.fna/markers.fasta)
[2023-06-28 22:49:18,955] [INFO] Task started: Blastn
[2023-06-28 22:49:18,955] [INFO] Running command: blastn -query GCA_027396995.1_ASM2739699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69336af0-2eef-4771-ac09-395c39262a92/dqc_reference/reference_markers_gtdb.fasta -out GCA_027396995.1_ASM2739699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:49:20,008] [INFO] Task succeeded: Blastn
[2023-06-28 22:49:20,013] [INFO] Selected 17 target genomes.
[2023-06-28 22:49:20,013] [INFO] Target genome list was writen to GCA_027396995.1_ASM2739699v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:49:20,018] [INFO] Task started: fastANI
[2023-06-28 22:49:20,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg709d8fd2-ea51-4c15-aefe-866226c71549/GCA_027396995.1_ASM2739699v1_genomic.fna.gz --refList GCA_027396995.1_ASM2739699v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027396995.1_ASM2739699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:49:29,537] [INFO] Task succeeded: fastANI
[2023-06-28 22:49:29,564] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 22:49:29,565] [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	78.5005	283	860	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	78.4349	269	860	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	78.4023	272	860	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_017883135.1	s__Bog-756 sp017883135	78.2389	238	860	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	78.2223	254	860	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_015478655.1	s__Bog-756 sp015478655	78.1153	238	860	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_903849265.1	s__Bog-756 sp903849265	78.0078	157	860	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_017883025.1	s__Bog-756 sp017883025	77.9453	219	860	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_903894295.1	s__Bog-756 sp903894295	77.8141	202	860	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_017883105.1	s__Bog-756 sp017883105	77.6994	152	860	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	77.6265	190	860	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_017882995.1	s__Chersky-840 sp017882995	77.4037	173	860	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_003157945.1	s__Bog-756 sp003157945	77.3901	167	860	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_003151955.1	s__PALSA-743 sp003151955	77.1141	243	860	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_003151235.1	s__Palsa-461 sp003151235	77.052	174	860	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Palsa-461	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161255.1	s__Palsa-461 sp003161255	76.9771	169	860	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Palsa-461	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003154135.1	s__UBA668 sp003154135	75.2199	66	860	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:49:29,567] [INFO] GTDB search result was written to GCA_027396995.1_ASM2739699v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:49:29,568] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:49:29,574] [INFO] DFAST_QC result json was written to GCA_027396995.1_ASM2739699v1_genomic.fna/dqc_result.json
[2023-06-28 22:49:29,575] [INFO] DFAST_QC completed!
[2023-06-28 22:49:29,575] [INFO] Total running time: 0h1m5s