[2023-06-28 12:03:46,566] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:03:46,569] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:03:46,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg6388b7fa-ed3c-4906-941d-c884f221099f/dqc_reference
[2023-06-28 12:03:47,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:03:47,952] [INFO] Task started: Prodigal
[2023-06-28 12:03:47,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg996fbbfa-7d54-4d50-b947-404f1f1319d2/GCA_019310385.1_ASM1931038v1_genomic.fna.gz | prodigal -d GCA_019310385.1_ASM1931038v1_genomic.fna/cds.fna -a GCA_019310385.1_ASM1931038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:04:01,208] [INFO] Task succeeded: Prodigal
[2023-06-28 12:04:01,209] [INFO] Task started: HMMsearch
[2023-06-28 12:04:01,209] [INFO] Running command: hmmsearch --tblout GCA_019310385.1_ASM1931038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6388b7fa-ed3c-4906-941d-c884f221099f/dqc_reference/reference_markers.hmm GCA_019310385.1_ASM1931038v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:04:01,526] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:04:01,528] [INFO] Found 6/6 markers.
[2023-06-28 12:04:01,581] [INFO] Query marker FASTA was written to GCA_019310385.1_ASM1931038v1_genomic.fna/markers.fasta
[2023-06-28 12:04:01,581] [INFO] Task started: Blastn
[2023-06-28 12:04:01,581] [INFO] Running command: blastn -query GCA_019310385.1_ASM1931038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6388b7fa-ed3c-4906-941d-c884f221099f/dqc_reference/reference_markers.fasta -out GCA_019310385.1_ASM1931038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:04:02,351] [INFO] Task succeeded: Blastn
[2023-06-28 12:04:02,355] [INFO] Selected 30 target genomes.
[2023-06-28 12:04:02,356] [INFO] Target genome list was writen to GCA_019310385.1_ASM1931038v1_genomic.fna/target_genomes.txt
[2023-06-28 12:04:02,360] [INFO] Task started: fastANI
[2023-06-28 12:04:02,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg996fbbfa-7d54-4d50-b947-404f1f1319d2/GCA_019310385.1_ASM1931038v1_genomic.fna.gz --refList GCA_019310385.1_ASM1931038v1_genomic.fna/target_genomes.txt --output GCA_019310385.1_ASM1931038v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:04:27,102] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:27,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6388b7fa-ed3c-4906-941d-c884f221099f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:04:27,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6388b7fa-ed3c-4906-941d-c884f221099f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:04:27,128] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:04:27,128] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:04:27,128] [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
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.3413	59	1543	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	75.2467	59	1543	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.2074	95	1543	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	75.2032	69	1543	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	75.1931	70	1543	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	75.1497	54	1543	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	75.1304	56	1543	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.0709	157	1543	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	75.059	87	1543	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	75.0016	101	1543	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	74.9896	157	1543	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.9885	153	1543	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	74.9465	96	1543	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	74.9326	140	1543	95	below_threshold
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	74.927	97	1543	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	74.8954	164	1543	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	74.8918	165	1543	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	74.8874	78	1543	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	74.8838	108	1543	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	74.8059	90	1543	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.7977	119	1543	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	74.7961	111	1543	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	74.7554	102	1543	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.7367	130	1543	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	74.6412	76	1543	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:04:27,130] [INFO] DFAST Taxonomy check result was written to GCA_019310385.1_ASM1931038v1_genomic.fna/tc_result.tsv
[2023-06-28 12:04:27,131] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:04:27,131] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:04:27,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6388b7fa-ed3c-4906-941d-c884f221099f/dqc_reference/checkm_data
[2023-06-28 12:04:27,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:04:27,184] [INFO] Task started: CheckM
[2023-06-28 12:04:27,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310385.1_ASM1931038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310385.1_ASM1931038v1_genomic.fna/checkm_input GCA_019310385.1_ASM1931038v1_genomic.fna/checkm_result
[2023-06-28 12:05:05,787] [INFO] Task succeeded: CheckM
[2023-06-28 12:05:05,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 12:05:05,815] [INFO] ===== Completeness check finished =====
[2023-06-28 12:05:05,815] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:05:05,816] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310385.1_ASM1931038v1_genomic.fna/markers.fasta)
[2023-06-28 12:05:05,816] [INFO] Task started: Blastn
[2023-06-28 12:05:05,816] [INFO] Running command: blastn -query GCA_019310385.1_ASM1931038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6388b7fa-ed3c-4906-941d-c884f221099f/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310385.1_ASM1931038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:05:07,127] [INFO] Task succeeded: Blastn
[2023-06-28 12:05:07,132] [INFO] Selected 20 target genomes.
[2023-06-28 12:05:07,132] [INFO] Target genome list was writen to GCA_019310385.1_ASM1931038v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:05:07,137] [INFO] Task started: fastANI
[2023-06-28 12:05:07,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg996fbbfa-7d54-4d50-b947-404f1f1319d2/GCA_019310385.1_ASM1931038v1_genomic.fna.gz --refList GCA_019310385.1_ASM1931038v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310385.1_ASM1931038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:05:23,613] [INFO] Task succeeded: fastANI
[2023-06-28 12:05:23,635] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:05:23,636] [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_002687015.1	s__GCA-2687015 sp002687015	76.838	275	1543	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__GCA-2687015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	76.5249	314	1543	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709835.1	s__UBA4427 sp002709835	76.4646	154	1543	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	76.2185	222	1543	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240165.1	s__JAZXM01 sp014240165	76.1795	134	1543	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JAZXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729515.1	s__GCA-2729515 sp002729515	76.1634	158	1543	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__GCA-2729515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875395.1	s__VGRF01 sp016875395	76.1505	189	1543	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.1309	306	1543	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262315.1	s__PR03 sp018262315	76.0503	140	1543	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	75.9756	250	1543	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339255.1	s__MYXO sp905339255	75.8838	139	1543	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA9160;g__MYXO	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862085.1	s__GCA-2862085 sp002862085	75.12	79	1543	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702545.1	s__JADJTL01 sp016702545	75.0594	105	1543	d__Bacteria;p__Myxococcota;c__Polyangia;o__GCA-2747355;f__GCA-2747355;g__JADJTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779205.1	s__GCA-2862085 sp016779205	75.0308	70	1543	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320815.1	s__UBA1660 sp002320815	74.9528	172	1543	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	99.96	99.96	0.96	0.96	2	-
GCA_016719295.1	s__JADKAF01 sp016719295	74.8502	145	1543	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793245.1	s__JADKAF01 sp016793245	74.7942	139	1543	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805845.1	s__Marmoricola_A sp902805845	74.6844	53	1543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:05:23,639] [INFO] GTDB search result was written to GCA_019310385.1_ASM1931038v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:05:23,639] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:05:23,648] [INFO] DFAST_QC result json was written to GCA_019310385.1_ASM1931038v1_genomic.fna/dqc_result.json
[2023-06-28 12:05:23,648] [INFO] DFAST_QC completed!
[2023-06-28 12:05:23,648] [INFO] Total running time: 0h1m37s