[2023-03-18 09:53:10,253] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:53:10,253] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:53:10,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg69636ce8-5363-4176-bb10-47f55af0aaa5/dqc_reference
[2023-03-18 09:53:11,428] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:53:11,428] [INFO] Task started: Prodigal
[2023-03-18 09:53:11,428] [INFO] Running command: cat /var/lib/cwl/stgbc720824-daa0-4ab9-920e-21e150f48f30/OceanDNA-b20925.fa | prodigal -d OceanDNA-b20925/cds.fna -a OceanDNA-b20925/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:54:08,885] [INFO] Task succeeded: Prodigal
[2023-03-18 09:54:08,885] [INFO] Task started: HMMsearch
[2023-03-18 09:54:08,885] [INFO] Running command: hmmsearch --tblout OceanDNA-b20925/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69636ce8-5363-4176-bb10-47f55af0aaa5/dqc_reference/reference_markers.hmm OceanDNA-b20925/protein.faa > /dev/null
[2023-03-18 09:54:09,238] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:54:09,239] [INFO] Found 6/6 markers.
[2023-03-18 09:54:09,293] [INFO] Query marker FASTA was written to OceanDNA-b20925/markers.fasta
[2023-03-18 09:54:09,294] [INFO] Task started: Blastn
[2023-03-18 09:54:09,294] [INFO] Running command: blastn -query OceanDNA-b20925/markers.fasta -db /var/lib/cwl/stg69636ce8-5363-4176-bb10-47f55af0aaa5/dqc_reference/reference_markers.fasta -out OceanDNA-b20925/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:54:10,059] [INFO] Task succeeded: Blastn
[2023-03-18 09:54:10,060] [INFO] Selected 35 target genomes.
[2023-03-18 09:54:10,060] [INFO] Target genome list was writen to OceanDNA-b20925/target_genomes.txt
[2023-03-18 09:54:10,076] [INFO] Task started: fastANI
[2023-03-18 09:54:10,077] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc720824-daa0-4ab9-920e-21e150f48f30/OceanDNA-b20925.fa --refList OceanDNA-b20925/target_genomes.txt --output OceanDNA-b20925/fastani_result.tsv --threads 1
[2023-03-18 09:54:48,133] [INFO] Task succeeded: fastANI
[2023-03-18 09:54:48,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69636ce8-5363-4176-bb10-47f55af0aaa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:54:48,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69636ce8-5363-4176-bb10-47f55af0aaa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:54:48,152] [INFO] Found 35 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:54:48,152] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:54:48,152] [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
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	76.4854	1379	3276	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.2456	914	3276	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.2103	835	3276	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.1944	842	3276	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1079	632	3276	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.0647	512	3276	95	below_threshold
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	75.023	104	3276	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	74.9766	268	3276	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	74.9751	185	3276	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	74.9322	132	3276	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	74.931	116	3276	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	74.9255	346	3276	95	below_threshold
Ornithinimicrobium avium	strain=AMA3305	GCA_003351765.1	2283195	2283195	type	True	74.9251	269	3276	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.9235	498	3276	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.9186	493	3276	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	74.9139	131	3276	95	below_threshold
Marmoricola solisilvae	strain=KIS18-7	GCA_003725775.1	1542737	1542737	type	True	74.9086	200	3276	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	74.908	346	3276	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	74.9051	228	3276	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	74.8977	174	3276	95	below_threshold
Nocardioides malaquae	strain=Y6	GCA_015070385.1	2773426	2773426	type	True	74.8937	186	3276	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	74.8831	302	3276	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	74.8707	114	3276	95	below_threshold
Glycomyces xiaoerkulensis	strain=TRM 41368	GCA_002798405.1	2038139	2038139	type	True	74.8544	237	3276	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.8454	277	3276	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	74.8431	387	3276	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	74.8344	243	3276	95	below_threshold
Bifidobacterium aesculapii	strain=DSM 26737	GCA_001417815.1	1329411	1329411	type	True	74.8129	94	3276	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	74.8128	196	3276	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	74.8095	355	3276	95	below_threshold
Micromonospora krabiensis	strain=DSM 45344	GCA_900091425.1	307121	307121	type	True	74.796	399	3276	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	74.7836	382	3276	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	74.7205	408	3276	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	74.7096	427	3276	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	74.701	334	3276	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:54:48,152] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20925/tc_result.tsv
[2023-03-18 09:54:48,152] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:54:48,152] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:54:48,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69636ce8-5363-4176-bb10-47f55af0aaa5/dqc_reference/checkm_data
[2023-03-18 09:54:48,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:54:48,163] [INFO] Task started: CheckM
[2023-03-18 09:54:48,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20925/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20925/checkm_input OceanDNA-b20925/checkm_result
[2023-03-18 09:58:12,870] [INFO] Task succeeded: CheckM
[2023-03-18 09:58:12,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:58:12,882] [INFO] ===== Completeness check finished =====
[2023-03-18 09:58:12,882] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:58:12,882] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20925/markers.fasta)
[2023-03-18 09:58:12,884] [INFO] Task started: Blastn
[2023-03-18 09:58:12,884] [INFO] Running command: blastn -query OceanDNA-b20925/markers.fasta -db /var/lib/cwl/stg69636ce8-5363-4176-bb10-47f55af0aaa5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20925/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:58:14,741] [INFO] Task succeeded: Blastn
[2023-03-18 09:58:14,742] [INFO] Selected 28 target genomes.
[2023-03-18 09:58:14,742] [INFO] Target genome list was writen to OceanDNA-b20925/target_genomes_gtdb.txt
[2023-03-18 09:58:14,794] [INFO] Task started: fastANI
[2023-03-18 09:58:14,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc720824-daa0-4ab9-920e-21e150f48f30/OceanDNA-b20925.fa --refList OceanDNA-b20925/target_genomes_gtdb.txt --output OceanDNA-b20925/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:59:03,929] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:03,945] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:59:03,945] [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_004213565.1	s__MED-G138 sp004213565	99.6582	2416	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__MED-G138	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000737325.1	s__Sandaracinus amylolyticus	76.493	1365	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699025.1	s__GCA-2699025 sp002699025	76.3885	1162	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__GCA-2699025	95.0	99.90	99.85	0.97	0.97	3	-
GCA_017644045.1	s__UBA1660 sp017644045	76.3876	913	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303575.1	s__JAFLCL01 sp017303575	76.2266	939	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__JAFLCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320815.1	s__UBA1660 sp002320815	76.2125	806	3276	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_012744445.1	s__JAAYBZ01 sp012744445	76.0634	533	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAAYBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151775.1	s__JAADHO01 sp013151775	76.043	471	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAADHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828805.1	s__Sandaracinus sp903828805	76.0303	582	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003647065.1	s__B10-G4 sp003647065	75.9981	451	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__B10-G4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706685.1	s__JADJJE01 sp016706685	75.8621	618	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JADJJE01	95.0	99.15	99.06	0.93	0.90	7	-
GCA_004297725.1	s__SCUS01 sp004297725	75.3706	735	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__SCUS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709545.1	s__JADJMO01 sp016709545	75.37	840	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJMO01;g__JADJMO01	95.0	95.09	95.09	0.90	0.90	2	-
GCA_004283055.1	s__SG8-38 sp004283055	75.3615	147	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	99.78	99.72	0.93	0.90	8	-
GCA_001899635.1	s__Labilithrix sp001899635	75.2809	747	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144635.1	s__Polyangium sp005144635	75.24	909	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649845.1	s__Polyangium spumosum	75.2105	830	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144585.1	s__Polyangium fumosum	75.1971	840	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696455.1	s__UBA2376 sp900696455	75.1718	833	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCF_000418325.1	s__Sorangium cellulosum_D	75.168	1161	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCA_016703425.1	s__JADJCA01 sp016703425	75.1647	485	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135735.1	s__Sorangium cellulosum_F	75.1256	995	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016190375.1	s__JACPQR01 sp016190375	75.1137	560	3276	d__Bacteria;p__Myxococcota;c__Polyangia;o__JACPQR01;f__JACPQR01;g__JACPQR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847385.1	s__CAINDO01 sp903847385	74.9616	623	3276	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA7976;f__UBA1532;g__CAINDO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874845.1	s__VGSZ01 sp016874845	74.9488	484	3276	d__Bacteria;p__Myxococcota;c__UBA727;o__UBA727;f__VGSZ01;g__VGSZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703525.1	s__JADJBW01 sp016703525	74.8584	208	3276	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__JADJBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879405.1	s__DP-19 sp005879405	74.8167	339	3276	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__UTPRO1;g__DP-19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900066015.1	s__Promineofilum breve	74.6268	119	3276	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__Promineofilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:59:03,946] [INFO] GTDB search result was written to OceanDNA-b20925/result_gtdb.tsv
[2023-03-18 09:59:03,946] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:59:03,949] [INFO] DFAST_QC result json was written to OceanDNA-b20925/dqc_result.json
[2023-03-18 09:59:03,949] [INFO] DFAST_QC completed!
[2023-03-18 09:59:03,949] [INFO] Total running time: 0h5m54s