[2023-06-18 23:42:55,484] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:42:55,506] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:42:55,506] [INFO] DQC Reference Directory: /var/lib/cwl/stgf518b69a-873e-4f55-ad29-dc771ad831cf/dqc_reference
[2023-06-18 23:42:57,800] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:42:57,801] [INFO] Task started: Prodigal
[2023-06-18 23:42:57,801] [INFO] Running command: gunzip -c /var/lib/cwl/stg28026250-03ee-4cca-9c91-3411fd676ac2/GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:43:02,821] [INFO] Task succeeded: Prodigal
[2023-06-18 23:43:02,822] [INFO] Task started: HMMsearch
[2023-06-18 23:43:02,822] [INFO] Running command: hmmsearch --tblout GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf518b69a-873e-4f55-ad29-dc771ad831cf/dqc_reference/reference_markers.hmm GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:43:02,971] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:43:02,972] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg28026250-03ee-4cca-9c91-3411fd676ac2/GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-18 23:43:03,029] [INFO] Query marker FASTA was written to GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 23:43:03,030] [INFO] Task started: Blastn
[2023-06-18 23:43:03,030] [INFO] Running command: blastn -query GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf518b69a-873e-4f55-ad29-dc771ad831cf/dqc_reference/reference_markers.fasta -out GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:43:05,299] [INFO] Task succeeded: Blastn
[2023-06-18 23:43:05,302] [INFO] Selected 19 target genomes.
[2023-06-18 23:43:05,303] [INFO] Target genome list was writen to GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 23:43:05,379] [INFO] Task started: fastANI
[2023-06-18 23:43:05,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg28026250-03ee-4cca-9c91-3411fd676ac2/GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:43:15,615] [INFO] Task succeeded: fastANI
[2023-06-18 23:43:15,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf518b69a-873e-4f55-ad29-dc771ad831cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:43:15,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf518b69a-873e-4f55-ad29-dc771ad831cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:43:15,630] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:43:15,630] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 23:43:15,630] [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
Sphingobium xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	79.5081	188	368	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	77.7744	127	368	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	77.7239	97	368	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	77.6368	86	368	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	77.5998	82	368	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	77.5839	99	368	95	below_threshold
Sphingobium herbicidovorans	strain=NBRC 16415	GCA_001598535.1	76947	76947	type	True	77.5213	78	368	95	below_threshold
Sphingobium herbicidovorans	strain=MH	GCA_002080435.1	76947	76947	type	True	77.5213	78	368	95	below_threshold
Sphingobium herbicidovorans	strain=NBRC 16415	GCA_000632125.2	76947	76947	type	True	77.492	78	368	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	77.4603	100	368	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	76.9768	68	368	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	76.9326	61	368	95	below_threshold
Sphingomonas aerolata	strain=NW12	GCA_003046295.1	185951	185951	type	True	76.9277	67	368	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	76.9142	68	368	95	below_threshold
Sphingomonas albertensis	strain=DOAB 1063	GCA_014358075.1	2762591	2762591	type	True	76.8998	56	368	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	76.8814	65	368	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.8789	67	368	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.7665	59	368	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 23:43:15,641] [INFO] DFAST Taxonomy check result was written to GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 23:43:15,641] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:43:15,642] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:43:15,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf518b69a-873e-4f55-ad29-dc771ad831cf/dqc_reference/checkm_data
[2023-06-18 23:43:15,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:43:15,666] [INFO] Task started: CheckM
[2023-06-18 23:43:15,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 23:43:36,018] [INFO] Task succeeded: CheckM
[2023-06-18 23:43:36,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:43:36,044] [INFO] ===== Completeness check finished =====
[2023-06-18 23:43:36,044] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:43:36,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 23:43:36,045] [INFO] Task started: Blastn
[2023-06-18 23:43:36,045] [INFO] Running command: blastn -query GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf518b69a-873e-4f55-ad29-dc771ad831cf/dqc_reference/reference_markers_gtdb.fasta -out GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:43:36,664] [INFO] Task succeeded: Blastn
[2023-06-18 23:43:36,668] [INFO] Selected 12 target genomes.
[2023-06-18 23:43:36,668] [INFO] Target genome list was writen to GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:43:36,701] [INFO] Task started: fastANI
[2023-06-18 23:43:36,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg28026250-03ee-4cca-9c91-3411fd676ac2/GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:43:43,820] [INFO] Task succeeded: fastANI
[2023-06-18 23:43:43,830] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 23:43:43,831] [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_017304105.1	s__Sphingobium sp017304105	79.2862	159	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201265.1	s__Sphingobium sp014201265	79.1473	142	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	3	-
GCA_017304655.1	s__Sphingobium sp017304655	79.0045	187	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603885.1	s__Sphingobium sp018603885	78.7635	188	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744605.1	s__Sphingobium sp017744605	78.5501	152	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899715.1	s__Sphingobium sp001899715	78.2716	178	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283515.1	s__Sphingobium sp000283515	78.1525	165	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.32	96.27	0.90	0.89	5	-
GCA_018823325.1	s__Sphingobium sp018823325	78.1474	153	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	0.97	0.94	4	-
GCF_000315525.1	s__Sphingobium yanoikuyae	77.7226	129	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_003591655.1	s__Sphingobium sp003591655	77.4195	101	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203965.1	s__Sphingobium sp014203965	77.3653	113	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003046295.1	s__Sphingomonas aerolata	76.9625	65	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.52	96.36	0.90	0.73	15	-
--------------------------------------------------------------------------------
[2023-06-18 23:43:43,833] [INFO] GTDB search result was written to GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 23:43:43,833] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:43:43,837] [INFO] DFAST_QC result json was written to GCA_937925445.1_SRR3901701_bin.2_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 23:43:43,837] [INFO] DFAST_QC completed!
[2023-06-18 23:43:43,837] [INFO] Total running time: 0h0m48s