[2023-06-30 07:54:31,173] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:54:31,216] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:54:31,216] [INFO] DQC Reference Directory: /var/lib/cwl/stg2765892c-45f0-4cf1-b972-fd54163fefdd/dqc_reference
[2023-06-30 07:54:34,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:54:34,402] [INFO] Task started: Prodigal
[2023-06-30 07:54:34,403] [INFO] Running command: gunzip -c /var/lib/cwl/stg4045f6f1-b0ed-4568-b542-177e985cbc85/GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna.gz | prodigal -d GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/cds.fna -a GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:54:44,975] [INFO] Task succeeded: Prodigal
[2023-06-30 07:54:44,976] [INFO] Task started: HMMsearch
[2023-06-30 07:54:44,976] [INFO] Running command: hmmsearch --tblout GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2765892c-45f0-4cf1-b972-fd54163fefdd/dqc_reference/reference_markers.hmm GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:54:45,258] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:54:45,260] [INFO] Found 6/6 markers.
[2023-06-30 07:54:45,299] [INFO] Query marker FASTA was written to GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/markers.fasta
[2023-06-30 07:54:45,300] [INFO] Task started: Blastn
[2023-06-30 07:54:45,300] [INFO] Running command: blastn -query GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/markers.fasta -db /var/lib/cwl/stg2765892c-45f0-4cf1-b972-fd54163fefdd/dqc_reference/reference_markers.fasta -out GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:54:46,095] [INFO] Task succeeded: Blastn
[2023-06-30 07:54:46,104] [INFO] Selected 19 target genomes.
[2023-06-30 07:54:46,105] [INFO] Target genome list was writen to GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/target_genomes.txt
[2023-06-30 07:54:46,108] [INFO] Task started: fastANI
[2023-06-30 07:54:46,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg4045f6f1-b0ed-4568-b542-177e985cbc85/GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna.gz --refList GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/target_genomes.txt --output GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:55:01,495] [INFO] Task succeeded: fastANI
[2023-06-30 07:55:01,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2765892c-45f0-4cf1-b972-fd54163fefdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:55:01,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2765892c-45f0-4cf1-b972-fd54163fefdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:55:01,518] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:55:01,519] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 07:55:01,519] [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
Geothrix fermentans	strain=DSM 14018	GCA_000428885.1	44676	44676	type	True	84.0169	724	1186	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	78.2194	297	1186	95	below_threshold
Thermithiobacillus tepidarius	strain=DSM 3134	GCA_000423825.1	929	929	type	True	75.5202	63	1186	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	75.4377	100	1186	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	75.4149	105	1186	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	75.3996	83	1186	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	75.3779	100	1186	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.3406	145	1186	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	75.3374	105	1186	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	75.3093	122	1186	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	75.1321	158	1186	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	75.1251	156	1186	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	75.0994	54	1186	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	75.0868	55	1186	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	74.9451	101	1186	95	below_threshold
Ornithinimicrobium pekingense	strain=CGMCC 1.5362	GCA_014644955.1	384677	384677	type	True	74.9155	70	1186	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	74.9155	70	1186	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	74.88	101	1186	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	74.8362	83	1186	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 07:55:01,526] [INFO] DFAST Taxonomy check result was written to GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/tc_result.tsv
[2023-06-30 07:55:01,527] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:55:01,527] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:55:01,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2765892c-45f0-4cf1-b972-fd54163fefdd/dqc_reference/checkm_data
[2023-06-30 07:55:01,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:55:01,593] [INFO] Task started: CheckM
[2023-06-30 07:55:01,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/checkm_input GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/checkm_result
[2023-06-30 07:55:36,687] [INFO] Task succeeded: CheckM
[2023-06-30 07:55:36,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 07:55:36,710] [INFO] ===== Completeness check finished =====
[2023-06-30 07:55:36,710] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:55:36,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/markers.fasta)
[2023-06-30 07:55:36,711] [INFO] Task started: Blastn
[2023-06-30 07:55:36,711] [INFO] Running command: blastn -query GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/markers.fasta -db /var/lib/cwl/stg2765892c-45f0-4cf1-b972-fd54163fefdd/dqc_reference/reference_markers_gtdb.fasta -out GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:55:37,879] [INFO] Task succeeded: Blastn
[2023-06-30 07:55:37,884] [INFO] Selected 7 target genomes.
[2023-06-30 07:55:37,884] [INFO] Target genome list was writen to GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:55:37,890] [INFO] Task started: fastANI
[2023-06-30 07:55:37,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg4045f6f1-b0ed-4568-b542-177e985cbc85/GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna.gz --refList GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/target_genomes_gtdb.txt --output GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:55:43,824] [INFO] Task succeeded: fastANI
[2023-06-30 07:55:43,838] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 07:55:43,838] [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_903857495.1	s__Geothrix sp903857495	99.9904	1165	1186	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.99	99.97	0.99	0.98	50	conclusive
GCA_903863195.1	s__Geothrix sp903863195	94.2589	916	1186	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.63	99.47	0.91	0.90	5	-
GCA_903937385.1	s__Geothrix sp903937385	93.6965	1029	1186	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.84	98.90	0.96	0.91	10	-
GCA_013334395.1	s__Geothrix sp013334395	92.2269	769	1186	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903843705.1	s__Geothrix sp903843705	90.9049	873	1186	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.09	98.86	0.88	0.85	6	-
GCA_903876615.1	s__Geothrix sp903876615	90.2548	544	1186	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903890595.1	s__Geothrix sp903890595	84.8385	608	1186	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.18	98.75	0.85	0.81	6	-
--------------------------------------------------------------------------------
[2023-06-30 07:55:43,860] [INFO] GTDB search result was written to GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/result_gtdb.tsv
[2023-06-30 07:55:43,861] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:55:43,867] [INFO] DFAST_QC result json was written to GCA_903832585.1_freshwater_MAG_---_MJ110516A_bin-827_genomic.fna/dqc_result.json
[2023-06-30 07:55:43,868] [INFO] DFAST_QC completed!
[2023-06-30 07:55:43,868] [INFO] Total running time: 0h1m13s