[2023-03-14 14:43:39,841] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:43:39,841] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:43:39,841] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb5f21c1-c2e2-4ca9-b5fa-f3cfb8115007/dqc_reference
[2023-03-14 14:43:45,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:43:45,832] [INFO] Task started: Prodigal
[2023-03-14 14:43:45,832] [INFO] Running command: cat /var/lib/cwl/stgd2b94787-d699-4c8f-aa7d-4d456948af5b/OceanDNA-b20922.fa | prodigal -d OceanDNA-b20922/cds.fna -a OceanDNA-b20922/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:44:52,250] [INFO] Task succeeded: Prodigal
[2023-03-14 14:44:52,250] [INFO] Task started: HMMsearch
[2023-03-14 14:44:52,250] [INFO] Running command: hmmsearch --tblout OceanDNA-b20922/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb5f21c1-c2e2-4ca9-b5fa-f3cfb8115007/dqc_reference/reference_markers.hmm OceanDNA-b20922/protein.faa > /dev/null
[2023-03-14 14:44:52,595] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:44:52,595] [INFO] Found 6/6 markers.
[2023-03-14 14:44:52,644] [INFO] Query marker FASTA was written to OceanDNA-b20922/markers.fasta
[2023-03-14 14:44:52,645] [INFO] Task started: Blastn
[2023-03-14 14:44:52,645] [INFO] Running command: blastn -query OceanDNA-b20922/markers.fasta -db /var/lib/cwl/stgbb5f21c1-c2e2-4ca9-b5fa-f3cfb8115007/dqc_reference/reference_markers.fasta -out OceanDNA-b20922/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:44:53,496] [INFO] Task succeeded: Blastn
[2023-03-14 14:44:53,498] [INFO] Selected 38 target genomes.
[2023-03-14 14:44:53,498] [INFO] Target genome list was writen to OceanDNA-b20922/target_genomes.txt
[2023-03-14 14:44:53,537] [INFO] Task started: fastANI
[2023-03-14 14:44:53,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2b94787-d699-4c8f-aa7d-4d456948af5b/OceanDNA-b20922.fa --refList OceanDNA-b20922/target_genomes.txt --output OceanDNA-b20922/fastani_result.tsv --threads 1
[2023-03-14 14:45:35,430] [INFO] Task succeeded: fastANI
[2023-03-14 14:45:35,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb5f21c1-c2e2-4ca9-b5fa-f3cfb8115007/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:45:35,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb5f21c1-c2e2-4ca9-b5fa-f3cfb8115007/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:45:35,516] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:45:35,516] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:45:35,516] [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	75.6541	814	2517	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.0986	452	2517	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.0676	396	2517	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.0675	270	2517	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.0629	356	2517	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.0462	437	2517	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.9891	444	2517	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.9853	459	2517	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	74.9798	58	2517	95	below_threshold
Luteimonas chenhongjianii	strain=100111	GCA_002327105.1	2006110	2006110	type	True	74.9768	69	2517	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	74.9616	127	2517	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	74.9367	69	2517	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	74.9297	68	2517	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.9296	239	2517	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	74.8905	156	2517	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	74.8599	114	2517	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	74.8308	91	2517	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	74.8291	87	2517	95	below_threshold
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	74.8214	90	2517	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	74.8127	145	2517	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	74.8087	145	2517	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	74.8055	147	2517	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	74.7898	70	2517	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	74.7898	70	2517	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	74.78	125	2517	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	74.7695	103	2517	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	74.7625	133	2517	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	74.7549	78	2517	95	below_threshold
Pseudonocardia abyssalis	strain=KRD168	GCA_019263705.2	2792008	2792008	type	True	74.7394	215	2517	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	74.7095	171	2517	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	74.7077	188	2517	95	below_threshold
Pseudonocardia sediminis	strain=DSM 45779	GCA_004217185.1	1397368	1397368	type	True	74.6872	209	2517	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	74.6653	164	2517	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:45:35,517] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20922/tc_result.tsv
[2023-03-14 14:45:35,517] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:45:35,518] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:45:35,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb5f21c1-c2e2-4ca9-b5fa-f3cfb8115007/dqc_reference/checkm_data
[2023-03-14 14:45:35,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:45:35,621] [INFO] Task started: CheckM
[2023-03-14 14:45:35,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20922/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20922/checkm_input OceanDNA-b20922/checkm_result
[2023-03-14 14:48:35,080] [INFO] Task succeeded: CheckM
[2023-03-14 14:48:35,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:48:35,084] [INFO] ===== Completeness check finished =====
[2023-03-14 14:48:35,084] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:48:35,085] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20922/markers.fasta)
[2023-03-14 14:48:35,086] [INFO] Task started: Blastn
[2023-03-14 14:48:35,086] [INFO] Running command: blastn -query OceanDNA-b20922/markers.fasta -db /var/lib/cwl/stgbb5f21c1-c2e2-4ca9-b5fa-f3cfb8115007/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20922/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:48:37,104] [INFO] Task succeeded: Blastn
[2023-03-14 14:48:37,105] [INFO] Selected 22 target genomes.
[2023-03-14 14:48:37,105] [INFO] Target genome list was writen to OceanDNA-b20922/target_genomes_gtdb.txt
[2023-03-14 14:48:37,129] [INFO] Task started: fastANI
[2023-03-14 14:48:37,129] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2b94787-d699-4c8f-aa7d-4d456948af5b/OceanDNA-b20922.fa --refList OceanDNA-b20922/target_genomes_gtdb.txt --output OceanDNA-b20922/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:49:00,181] [INFO] Task succeeded: fastANI
[2023-03-14 14:49:00,193] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:49:00,193] [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_002699025.1	s__GCA-2699025 sp002699025	77.0836	848	2517	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	76.7646	726	2517	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_002320815.1	s__UBA1660 sp002320815	76.697	569	2517	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_009992505.1	s__JAADHO01 sp009992505	76.1764	253	2517	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_016706685.1	s__JADJJE01 sp016706685	76.1564	433	2517	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_013151775.1	s__JAADHO01 sp013151775	76.1075	321	2517	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_012744445.1	s__JAAYBZ01 sp012744445	76.0635	329	2517	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_003647065.1	s__B10-G4 sp003647065	75.7485	253	2517	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	-
GCF_000737325.1	s__Sandaracinus amylolyticus	75.6486	813	2517	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303575.1	s__JAFLCL01 sp017303575	75.5191	590	2517	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__JAFLCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881055.1	s__JADGRF01 sp017881055	75.4206	266	2517	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JAFGIB01;g__JADGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003647035.1	s__SG8-38 sp003647035	75.4044	98	2517	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	96.70	96.70	0.74	0.74	2	-
GCA_017881145.1	s__JADGRF01 sp017881145	75.3924	137	2517	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JAFGIB01;g__JADGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881185.1	s__JADGRF01 sp017881185	75.3526	223	2517	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JAFGIB01;g__JADGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719945.1	s__CAITIQ01 sp016719945	75.148	376	2517	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITIQ01	95.0	99.43	99.43	0.95	0.95	2	-
GCF_900172345.1	s__Limimaricola soesokkakensis	74.8214	90	2517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002050235.1	s__UTPRO1 sp002050235	74.8199	134	2517	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__UTPRO1;g__UTPRO1	95.0	99.98	99.98	0.96	0.96	2	-
GCA_012719255.1	s__Gulosibacter sp012719255	74.7764	144	2517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719445.1	s__JAAYAH01 sp012719445	74.7372	81	2517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JAAYAH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879205.1	s__DP-3 sp005879205	74.7369	140	2517	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200155.1	s__SIAQ01 sp016200155	74.6826	50	2517	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:49:00,193] [INFO] GTDB search result was written to OceanDNA-b20922/result_gtdb.tsv
[2023-03-14 14:49:00,194] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:49:00,198] [INFO] DFAST_QC result json was written to OceanDNA-b20922/dqc_result.json
[2023-03-14 14:49:00,199] [INFO] DFAST_QC completed!
[2023-03-14 14:49:00,199] [INFO] Total running time: 0h5m20s