[2023-06-30 21:55:00,798] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:55:00,801] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:55:00,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e1294f2-b1aa-4fc9-aea6-eec64e807ca0/dqc_reference
[2023-06-30 21:55:02,260] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:55:02,261] [INFO] Task started: Prodigal
[2023-06-30 21:55:02,261] [INFO] Running command: gunzip -c /var/lib/cwl/stg09dfbc62-d65a-44eb-8dec-0ffb22367cec/GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna.gz | prodigal -d GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/cds.fna -a GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:55:13,948] [INFO] Task succeeded: Prodigal
[2023-06-30 21:55:13,949] [INFO] Task started: HMMsearch
[2023-06-30 21:55:13,949] [INFO] Running command: hmmsearch --tblout GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e1294f2-b1aa-4fc9-aea6-eec64e807ca0/dqc_reference/reference_markers.hmm GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:55:14,282] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:55:14,283] [INFO] Found 6/6 markers.
[2023-06-30 21:55:14,334] [INFO] Query marker FASTA was written to GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/markers.fasta
[2023-06-30 21:55:14,335] [INFO] Task started: Blastn
[2023-06-30 21:55:14,335] [INFO] Running command: blastn -query GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e1294f2-b1aa-4fc9-aea6-eec64e807ca0/dqc_reference/reference_markers.fasta -out GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:55:14,980] [INFO] Task succeeded: Blastn
[2023-06-30 21:55:14,985] [INFO] Selected 37 target genomes.
[2023-06-30 21:55:14,985] [INFO] Target genome list was writen to GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/target_genomes.txt
[2023-06-30 21:55:15,058] [INFO] Task started: fastANI
[2023-06-30 21:55:15,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg09dfbc62-d65a-44eb-8dec-0ffb22367cec/GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna.gz --refList GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/target_genomes.txt --output GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:55:48,560] [INFO] Task succeeded: fastANI
[2023-06-30 21:55:48,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e1294f2-b1aa-4fc9-aea6-eec64e807ca0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:55:48,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e1294f2-b1aa-4fc9-aea6-eec64e807ca0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:55:48,582] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:55:48,583] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 21:55:48,583] [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
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.3132	115	1630	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	74.9379	64	1630	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	74.8955	63	1630	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	74.8646	130	1630	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.8626	200	1630	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	74.8571	149	1630	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	74.8256	223	1630	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	74.8192	131	1630	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	74.8167	215	1630	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_018398275.1	28210	28210	type	True	74.7889	59	1630	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_003201475.1	28210	28210	type	True	74.7889	59	1630	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	74.7857	138	1630	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	74.7733	113	1630	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	74.773	51	1630	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	74.7717	133	1630	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	74.7685	120	1630	95	below_threshold
Nocardioides speluncae	strain=YIM ART13	GCA_003121585.1	2670337	2670337	type	True	74.7634	96	1630	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	74.7612	147	1630	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	74.7573	181	1630	95	below_threshold
Streptomyces sparsogenes	strain=DSM 40356	GCA_001969965.1	67365	67365	type	True	74.7536	184	1630	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	74.7508	197	1630	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_008630015.1	140057	140057	type	True	74.7453	55	1630	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	74.7453	55	1630	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	74.7436	181	1630	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	74.7384	56	1630	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	74.7269	114	1630	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_000721235.1	47716	47716	type	True	74.7221	173	1630	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	74.7162	148	1630	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	74.7144	178	1630	95	below_threshold
Halolamina rubra	strain=CBA1107	GCA_000739555.1	1380430	1380430	type	True	74.6437	83	1630	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 21:55:48,585] [INFO] DFAST Taxonomy check result was written to GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/tc_result.tsv
[2023-06-30 21:55:48,586] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:55:48,586] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:55:48,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e1294f2-b1aa-4fc9-aea6-eec64e807ca0/dqc_reference/checkm_data
[2023-06-30 21:55:48,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:55:48,641] [INFO] Task started: CheckM
[2023-06-30 21:55:48,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/checkm_input GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/checkm_result
[2023-06-30 21:56:27,473] [INFO] Task succeeded: CheckM
[2023-06-30 21:56:27,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.67%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:56:27,499] [INFO] ===== Completeness check finished =====
[2023-06-30 21:56:27,500] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:56:27,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/markers.fasta)
[2023-06-30 21:56:27,501] [INFO] Task started: Blastn
[2023-06-30 21:56:27,501] [INFO] Running command: blastn -query GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e1294f2-b1aa-4fc9-aea6-eec64e807ca0/dqc_reference/reference_markers_gtdb.fasta -out GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:56:28,425] [INFO] Task succeeded: Blastn
[2023-06-30 21:56:28,429] [INFO] Selected 11 target genomes.
[2023-06-30 21:56:28,429] [INFO] Target genome list was writen to GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:56:28,439] [INFO] Task started: fastANI
[2023-06-30 21:56:28,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg09dfbc62-d65a-44eb-8dec-0ffb22367cec/GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna.gz --refList GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/target_genomes_gtdb.txt --output GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:56:39,669] [INFO] Task succeeded: fastANI
[2023-06-30 21:56:39,680] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:56:39,681] [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_903845115.1	s__CAIMWE01 sp903845115	99.7949	1522	1630	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__CAIMWE01	95.0	99.85	99.67	0.96	0.93	7	conclusive
GCA_016716705.1	s__UBA5066 sp016716705	78.5992	500	1630	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__UBA5066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008363385.1	s__RHKY01 sp008363385	78.5894	591	1630	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__RHKY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714815.1	s__UBA5066 sp016714815	78.4093	592	1630	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__UBA5066	95.0	99.07	99.07	0.92	0.92	2	-
GCA_016719485.1	s__UBA5066 sp016719485	78.3525	518	1630	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__UBA5066	95.0	97.48	97.48	0.88	0.88	2	-
GCA_017999215.1	s__UBA5066 sp017999215	78.3138	424	1630	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__UBA5066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716715.1	s__Fen-183 sp016716715	77.6531	406	1630	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__Fen-183	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003152095.1	s__Fen-183 sp003152095	77.2879	284	1630	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__Fen-183	95.0	99.53	99.53	0.90	0.90	2	-
GCA_016184455.1	s__Gp6-AA40 sp016184455	75.0028	101	1630	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863495.1	s__Micromonospora andamanensis	74.8231	109	1630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_014204895.1	s__Actinoplanes abujensis	74.7603	139	1630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-30 21:56:39,683] [INFO] GTDB search result was written to GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/result_gtdb.tsv
[2023-06-30 21:56:39,684] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:56:39,691] [INFO] DFAST_QC result json was written to GCA_903906115.1_freshwater_MAG_---_AM-lipid-01-D8_bin-0234_genomic.fna/dqc_result.json
[2023-06-30 21:56:39,692] [INFO] DFAST_QC completed!
[2023-06-30 21:56:39,692] [INFO] Total running time: 0h1m39s