[2023-06-16 21:53:24,027] [INFO] DFAST_QC pipeline started.
[2023-06-16 21:53:24,029] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 21:53:24,029] [INFO] DQC Reference Directory: /var/lib/cwl/stgecc0780f-a2bd-4e3c-95da-3a2530048b88/dqc_reference
[2023-06-16 21:53:25,508] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 21:53:25,509] [INFO] Task started: Prodigal
[2023-06-16 21:53:25,509] [INFO] Running command: gunzip -c /var/lib/cwl/stg00d65354-5c4d-47c4-8969-3b822a8ef6c7/GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna.gz | prodigal -d GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/cds.fna -a GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 21:53:36,516] [INFO] Task succeeded: Prodigal
[2023-06-16 21:53:36,516] [INFO] Task started: HMMsearch
[2023-06-16 21:53:36,517] [INFO] Running command: hmmsearch --tblout GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecc0780f-a2bd-4e3c-95da-3a2530048b88/dqc_reference/reference_markers.hmm GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/protein.faa > /dev/null
[2023-06-16 21:53:36,807] [INFO] Task succeeded: HMMsearch
[2023-06-16 21:53:36,808] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg00d65354-5c4d-47c4-8969-3b822a8ef6c7/GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna.gz]
[2023-06-16 21:53:36,854] [INFO] Query marker FASTA was written to GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/markers.fasta
[2023-06-16 21:53:36,854] [INFO] Task started: Blastn
[2023-06-16 21:53:36,855] [INFO] Running command: blastn -query GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecc0780f-a2bd-4e3c-95da-3a2530048b88/dqc_reference/reference_markers.fasta -out GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:53:37,636] [INFO] Task succeeded: Blastn
[2023-06-16 21:53:37,648] [INFO] Selected 31 target genomes.
[2023-06-16 21:53:37,649] [INFO] Target genome list was writen to GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/target_genomes.txt
[2023-06-16 21:53:37,718] [INFO] Task started: fastANI
[2023-06-16 21:53:37,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg00d65354-5c4d-47c4-8969-3b822a8ef6c7/GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna.gz --refList GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/target_genomes.txt --output GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 21:54:05,276] [INFO] Task succeeded: fastANI
[2023-06-16 21:54:05,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecc0780f-a2bd-4e3c-95da-3a2530048b88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 21:54:05,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecc0780f-a2bd-4e3c-95da-3a2530048b88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 21:54:05,295] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 21:54:05,295] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 21:54:05,295] [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
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.1738	106	1478	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	75.1331	72	1478	95	below_threshold
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.1211	92	1478	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	75.1208	50	1478	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.0549	121	1478	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	74.9924	81	1478	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	74.9709	55	1478	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.9692	125	1478	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	74.9503	151	1478	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.9414	116	1478	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.9319	128	1478	95	below_threshold
Nocardioides cynanchi	strain=SB3-45	GCA_008761635.1	2558918	2558918	type	True	74.9156	93	1478	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	74.9117	62	1478	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	74.9007	88	1478	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	74.8833	106	1478	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	74.864	101	1478	95	below_threshold
Methylobacterium phyllostachyos	strain=BL47	GCA_900103445.1	582672	582672	type	True	74.8637	100	1478	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.8637	173	1478	95	below_threshold
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	74.8595	151	1478	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	74.826	163	1478	95	below_threshold
Halorhodospira halophila	strain=SL1	GCA_000015585.1	1053	1053	suspected-type	True	74.826	60	1478	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	74.8205	164	1478	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	74.7644	105	1478	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	74.7643	164	1478	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 21:54:05,297] [INFO] DFAST Taxonomy check result was written to GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/tc_result.tsv
[2023-06-16 21:54:05,298] [INFO] ===== Taxonomy check completed =====
[2023-06-16 21:54:05,298] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 21:54:05,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecc0780f-a2bd-4e3c-95da-3a2530048b88/dqc_reference/checkm_data
[2023-06-16 21:54:05,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 21:54:05,352] [INFO] Task started: CheckM
[2023-06-16 21:54:05,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/checkm_input GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/checkm_result
[2023-06-16 21:54:40,546] [INFO] Task succeeded: CheckM
[2023-06-16 21:54:40,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:54:40,572] [INFO] ===== Completeness check finished =====
[2023-06-16 21:54:40,572] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:54:40,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/markers.fasta)
[2023-06-16 21:54:40,573] [INFO] Task started: Blastn
[2023-06-16 21:54:40,573] [INFO] Running command: blastn -query GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecc0780f-a2bd-4e3c-95da-3a2530048b88/dqc_reference/reference_markers_gtdb.fasta -out GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:54:41,767] [INFO] Task succeeded: Blastn
[2023-06-16 21:54:41,772] [INFO] Selected 24 target genomes.
[2023-06-16 21:54:41,772] [INFO] Target genome list was writen to GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:54:41,784] [INFO] Task started: fastANI
[2023-06-16 21:54:41,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg00d65354-5c4d-47c4-8969-3b822a8ef6c7/GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna.gz --refList GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/target_genomes_gtdb.txt --output GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:55:00,474] [INFO] Task succeeded: fastANI
[2023-06-16 21:55:00,503] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 21:55:00,503] [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_905479655.1	s__CAJQNK01 sp905479655	100.0	1459	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__CAJQNK01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012521815.1	s__JAAYLR01 sp012521815	76.2123	184	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	99.12	98.38	0.89	0.78	5	-
GCA_014584695.1	s__JACTMI01 sp014584695	76.1187	258	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837085.1	s__WTGL01 sp009837085	76.0636	138	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.78	99.78	0.96	0.95	3	-
GCA_016699405.1	s__JAAYLR01 sp016699405	76.0238	250	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525905.1	s__JACTMI01 sp011525905	76.0134	249	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860005.1	s__JACTMI01 sp017860005	76.0101	249	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009845425.1	s__WTGL01 sp009845425	76.0092	157	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.99	99.99	0.99	0.99	3	-
GCA_018057705.1	s__JAGPDF01 sp018057705	75.9435	207	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAGPDF01	95.0	99.73	99.73	0.94	0.94	2	-
GCA_009837885.1	s__WTGL01 sp009837885	75.9375	160	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.92	99.92	0.99	0.99	2	-
GCA_003697015.1	s__J023 sp003697015	75.9216	320	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009843505.1	s__WTGL01 sp009843505	75.9054	142	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_003388555.1	s__QQVD01 sp003388555	75.6805	269	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_008363385.1	s__RHKY01 sp008363385	75.2174	201	1478	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__RHKY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192275.1	s__Halomonas stenophila	74.9371	103	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355415.1	s__Sulfurifustis variabilis	74.8848	70	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfurifustis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004328075.1	s__Siculibacillus lacustris	74.8506	107	1478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Siculibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381945.1	s__Thioalkalivibrio sp000381945	74.8367	52	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752535.1	s__Tautonia plasticadhaerens	74.804	187	1478	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514535.1	s__NIC37A-2 sp012514535	74.8014	94	1478	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__NIC37A-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140175.1	s__PALSA-555 sp003140175	74.6265	83	1478	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__PALSA-555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133145.1	s__T1Sed10-49 sp007133145	74.6259	75	1478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__T1Sed10-49	95.0	98.98	98.60	0.85	0.78	3	-
--------------------------------------------------------------------------------
[2023-06-16 21:55:00,505] [INFO] GTDB search result was written to GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/result_gtdb.tsv
[2023-06-16 21:55:00,506] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:55:00,511] [INFO] DFAST_QC result json was written to GCA_905479655.1_10_20180412_Bin_METABAT_171_1_genomic.fna/dqc_result.json
[2023-06-16 21:55:00,511] [INFO] DFAST_QC completed!
[2023-06-16 21:55:00,511] [INFO] Total running time: 0h1m36s