[2023-06-13 12:39:43,965] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:39:43,970] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:39:43,971] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e94aa98-cba9-45ea-8b7e-b77fbc3f4927/dqc_reference
[2023-06-13 12:39:45,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:39:45,208] [INFO] Task started: Prodigal
[2023-06-13 12:39:45,208] [INFO] Running command: gunzip -c /var/lib/cwl/stg0de1a70f-66a8-483d-9dde-dd4982f42826/GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:40:15,889] [INFO] Task succeeded: Prodigal
[2023-06-13 12:40:15,889] [INFO] Task started: HMMsearch
[2023-06-13 12:40:15,889] [INFO] Running command: hmmsearch --tblout GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e94aa98-cba9-45ea-8b7e-b77fbc3f4927/dqc_reference/reference_markers.hmm GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:40:16,337] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:40:16,338] [INFO] Found 6/6 markers.
[2023-06-13 12:40:16,425] [INFO] Query marker FASTA was written to GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 12:40:16,426] [INFO] Task started: Blastn
[2023-06-13 12:40:16,426] [INFO] Running command: blastn -query GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e94aa98-cba9-45ea-8b7e-b77fbc3f4927/dqc_reference/reference_markers.fasta -out GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:40:17,195] [INFO] Task succeeded: Blastn
[2023-06-13 12:40:17,200] [INFO] Selected 27 target genomes.
[2023-06-13 12:40:17,200] [INFO] Target genome list was writen to GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 12:40:17,205] [INFO] Task started: fastANI
[2023-06-13 12:40:17,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg0de1a70f-66a8-483d-9dde-dd4982f42826/GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:40:47,203] [INFO] Task succeeded: fastANI
[2023-06-13 12:40:47,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e94aa98-cba9-45ea-8b7e-b77fbc3f4927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:40:47,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e94aa98-cba9-45ea-8b7e-b77fbc3f4927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:40:47,230] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 12:40:47,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 12:40:47,230] [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
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	78.6563	1325	3771	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.8537	813	3771	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.8239	824	3771	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.7804	778	3771	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.4736	487	3771	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.3803	1062	3771	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	74.9743	208	3771	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	74.9328	139	3771	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	74.859	208	3771	95	below_threshold
Intrasporangium calvum	strain=DSM 43043	GCA_000184685.1	53358	53358	type	True	74.8482	181	3771	95	below_threshold
Burkholderia thailandensis	strain=E264	GCA_003568605.1	57975	57975	type	True	74.8141	430	3771	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	74.8028	182	3771	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	74.8014	319	3771	95	below_threshold
Burkholderia thailandensis	strain=E264; ATCC 700388	GCA_000012365.1	57975	57975	type	True	74.7997	435	3771	95	below_threshold
Burkholderia thailandensis	strain=ATCC 700388	GCA_000152285.1	57975	57975	type	True	74.7838	418	3771	95	below_threshold
Agrococcus casei	strain=LMG 22410	GCA_900163565.1	343512	343512	type	True	74.779	92	3771	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	74.7664	153	3771	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	74.7538	355	3771	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	74.7492	337	3771	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	74.7444	302	3771	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	74.7157	161	3771	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	74.7152	163	3771	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	74.6734	273	3771	95	below_threshold
Mycolicibacterium aichiense	strain=NCTC10820	GCA_900453085.1	1799	1799	type	True	74.6721	123	3771	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	74.6674	272	3771	95	below_threshold
Mycolicibacterium aichiense	strain=JCM 6376	GCA_010726245.1	1799	1799	type	True	74.6494	124	3771	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	74.6004	154	3771	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 12:40:47,232] [INFO] DFAST Taxonomy check result was written to GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 12:40:47,233] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:40:47,233] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:40:47,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e94aa98-cba9-45ea-8b7e-b77fbc3f4927/dqc_reference/checkm_data
[2023-06-13 12:40:47,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:40:47,363] [INFO] Task started: CheckM
[2023-06-13 12:40:47,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 12:42:19,500] [INFO] Task succeeded: CheckM
[2023-06-13 12:42:19,502] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 12:42:19,536] [INFO] ===== Completeness check finished =====
[2023-06-13 12:42:19,536] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:42:19,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 12:42:19,537] [INFO] Task started: Blastn
[2023-06-13 12:42:19,537] [INFO] Running command: blastn -query GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e94aa98-cba9-45ea-8b7e-b77fbc3f4927/dqc_reference/reference_markers_gtdb.fasta -out GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:42:20,756] [INFO] Task succeeded: Blastn
[2023-06-13 12:42:20,761] [INFO] Selected 19 target genomes.
[2023-06-13 12:42:20,761] [INFO] Target genome list was writen to GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:42:20,769] [INFO] Task started: fastANI
[2023-06-13 12:42:20,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg0de1a70f-66a8-483d-9dde-dd4982f42826/GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:42:50,411] [INFO] Task succeeded: fastANI
[2023-06-13 12:42:50,429] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 12:42:50,429] [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_001899635.1	s__Labilithrix sp001899635	99.9904	3750	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001263205.1	s__Labilithrix luteola	78.6499	1324	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009781005.1	s__Labilithrix sp009781005	77.1003	406	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712525.1	s__JAAFHV01 sp016712525	76.9921	863	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720545.1	s__JAAFHV01 sp016720545	76.6962	779	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	99.45	99.45	0.94	0.94	2	-
GCA_005777185.1	s__SXNL01 sp005777185	76.6609	712	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__SXNL01	95.0	99.91	99.91	0.95	0.95	3	-
GCA_013297655.1	s__JAAFHV01 sp013297655	76.565	805	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153495.1	s__Palsa-1150 sp003153495	76.4579	398	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Palsa-1150	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709545.1	s__JADJMO01 sp016709545	75.8887	763	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJMO01;g__JADJMO01	95.0	95.09	95.09	0.90	0.90	2	-
GCA_903906315.1	s__CAIVJW01 sp903906315	75.8289	844	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIVJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361525.1	s__CAITIQ01 sp013361525	75.6942	671	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITIQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870415.1	s__CAIQDA01 sp903870415	75.6872	192	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIQDA01	95.0	99.68	99.68	0.92	0.92	2	-
GCF_000601485.1	s__Chondromyces apiculatus	75.5312	550	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Chondromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075635.1	s__JADJKB01 sp015075635	75.437	525	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJKB01	95.0	96.31	96.31	0.86	0.86	2	-
GCA_017303575.1	s__JAFLCL01 sp017303575	75.4005	688	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__JAFLCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191785.1	s__JADJKB01 sp016191785	75.2995	437	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001465015.1	s__Ga0077539 sp001465015	75.1394	524	3771	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__Ga0077539	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	74.868	492	3771	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 12:42:50,431] [INFO] GTDB search result was written to GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 12:42:50,432] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:42:50,437] [INFO] DFAST_QC result json was written to GCA_938005665.1_SRR3901695_bin.44_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 12:42:50,437] [INFO] DFAST_QC completed!
[2023-06-13 12:42:50,437] [INFO] Total running time: 0h3m6s