[2023-06-17 17:24:06,910] [INFO] DFAST_QC pipeline started.
[2023-06-17 17:24:06,914] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 17:24:06,914] [INFO] DQC Reference Directory: /var/lib/cwl/stg51b1a8f5-0ee8-4a5f-91e0-cdf99cbaafd0/dqc_reference
[2023-06-17 17:24:08,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 17:24:08,158] [INFO] Task started: Prodigal
[2023-06-17 17:24:08,158] [INFO] Running command: gunzip -c /var/lib/cwl/stgc46add80-43bd-4192-8ff5-b7416f89e698/GCA_009840205.1_ASM984020v1_genomic.fna.gz | prodigal -d GCA_009840205.1_ASM984020v1_genomic.fna/cds.fna -a GCA_009840205.1_ASM984020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 17:24:18,987] [INFO] Task succeeded: Prodigal
[2023-06-17 17:24:18,988] [INFO] Task started: HMMsearch
[2023-06-17 17:24:18,988] [INFO] Running command: hmmsearch --tblout GCA_009840205.1_ASM984020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51b1a8f5-0ee8-4a5f-91e0-cdf99cbaafd0/dqc_reference/reference_markers.hmm GCA_009840205.1_ASM984020v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 17:24:19,264] [INFO] Task succeeded: HMMsearch
[2023-06-17 17:24:19,266] [INFO] Found 6/6 markers.
[2023-06-17 17:24:19,303] [INFO] Query marker FASTA was written to GCA_009840205.1_ASM984020v1_genomic.fna/markers.fasta
[2023-06-17 17:24:19,303] [INFO] Task started: Blastn
[2023-06-17 17:24:19,303] [INFO] Running command: blastn -query GCA_009840205.1_ASM984020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51b1a8f5-0ee8-4a5f-91e0-cdf99cbaafd0/dqc_reference/reference_markers.fasta -out GCA_009840205.1_ASM984020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 17:24:19,958] [INFO] Task succeeded: Blastn
[2023-06-17 17:24:19,965] [INFO] Selected 25 target genomes.
[2023-06-17 17:24:19,966] [INFO] Target genome list was writen to GCA_009840205.1_ASM984020v1_genomic.fna/target_genomes.txt
[2023-06-17 17:24:19,970] [INFO] Task started: fastANI
[2023-06-17 17:24:19,971] [INFO] Running command: fastANI --query /var/lib/cwl/stgc46add80-43bd-4192-8ff5-b7416f89e698/GCA_009840205.1_ASM984020v1_genomic.fna.gz --refList GCA_009840205.1_ASM984020v1_genomic.fna/target_genomes.txt --output GCA_009840205.1_ASM984020v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 17:24:42,084] [INFO] Task succeeded: fastANI
[2023-06-17 17:24:42,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51b1a8f5-0ee8-4a5f-91e0-cdf99cbaafd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 17:24:42,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51b1a8f5-0ee8-4a5f-91e0-cdf99cbaafd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 17:24:42,104] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 17:24:42,104] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 17:24:42,104] [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	75.3771	95	1437	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	75.2299	63	1437	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	75.2246	74	1437	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.212	111	1437	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.1906	93	1437	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	75.0252	112	1437	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.9427	111	1437	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	74.9228	220	1437	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	74.9094	186	1437	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	74.8938	194	1437	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.8917	137	1437	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	74.8808	76	1437	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	74.8503	99	1437	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	74.8253	158	1437	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	74.8172	86	1437	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.8139	127	1437	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	74.8127	145	1437	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	74.761	108	1437	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 17:24:42,106] [INFO] DFAST Taxonomy check result was written to GCA_009840205.1_ASM984020v1_genomic.fna/tc_result.tsv
[2023-06-17 17:24:42,107] [INFO] ===== Taxonomy check completed =====
[2023-06-17 17:24:42,107] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 17:24:42,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51b1a8f5-0ee8-4a5f-91e0-cdf99cbaafd0/dqc_reference/checkm_data
[2023-06-17 17:24:42,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 17:24:42,153] [INFO] Task started: CheckM
[2023-06-17 17:24:42,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009840205.1_ASM984020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009840205.1_ASM984020v1_genomic.fna/checkm_input GCA_009840205.1_ASM984020v1_genomic.fna/checkm_result
[2023-06-17 17:25:17,015] [INFO] Task succeeded: CheckM
[2023-06-17 17:25:17,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 17:25:17,043] [INFO] ===== Completeness check finished =====
[2023-06-17 17:25:17,043] [INFO] ===== Start GTDB Search =====
[2023-06-17 17:25:17,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009840205.1_ASM984020v1_genomic.fna/markers.fasta)
[2023-06-17 17:25:17,044] [INFO] Task started: Blastn
[2023-06-17 17:25:17,044] [INFO] Running command: blastn -query GCA_009840205.1_ASM984020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51b1a8f5-0ee8-4a5f-91e0-cdf99cbaafd0/dqc_reference/reference_markers_gtdb.fasta -out GCA_009840205.1_ASM984020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 17:25:18,037] [INFO] Task succeeded: Blastn
[2023-06-17 17:25:18,043] [INFO] Selected 7 target genomes.
[2023-06-17 17:25:18,043] [INFO] Target genome list was writen to GCA_009840205.1_ASM984020v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 17:25:18,082] [INFO] Task started: fastANI
[2023-06-17 17:25:18,082] [INFO] Running command: fastANI --query /var/lib/cwl/stgc46add80-43bd-4192-8ff5-b7416f89e698/GCA_009840205.1_ASM984020v1_genomic.fna.gz --refList GCA_009840205.1_ASM984020v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009840205.1_ASM984020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 17:25:26,180] [INFO] Task succeeded: fastANI
[2023-06-17 17:25:26,194] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 17:25:26,194] [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_009836625.1	s__WTGL01 sp009836625	98.0299	1308	1437	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.03	98.03	0.95	0.91	5	conclusive
GCA_009845425.1	s__WTGL01 sp009845425	94.652	1282	1437	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.99	99.99	0.99	0.99	3	-
GCA_009837885.1	s__WTGL01 sp009837885	92.8218	1242	1437	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.92	99.92	0.99	0.99	2	-
GCA_009843505.1	s__WTGL01 sp009843505	92.2597	1248	1437	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_011525365.1	s__WTGL01 sp011525365	92.1819	1228	1437	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837085.1	s__WTGL01 sp009837085	91.8553	1142	1437	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.78	99.78	0.96	0.95	3	-
GCA_012270995.1	s__WTGL01 sp012270995	87.7269	1071	1437	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 17:25:26,197] [INFO] GTDB search result was written to GCA_009840205.1_ASM984020v1_genomic.fna/result_gtdb.tsv
[2023-06-17 17:25:26,197] [INFO] ===== GTDB Search completed =====
[2023-06-17 17:25:26,201] [INFO] DFAST_QC result json was written to GCA_009840205.1_ASM984020v1_genomic.fna/dqc_result.json
[2023-06-17 17:25:26,201] [INFO] DFAST_QC completed!
[2023-06-17 17:25:26,201] [INFO] Total running time: 0h1m19s