[2023-06-29 20:14:24,286] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:14:24,288] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:14:24,288] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0fa29f2-9316-485f-98d3-1fda5e040add/dqc_reference
[2023-06-29 20:14:25,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:14:25,681] [INFO] Task started: Prodigal
[2023-06-29 20:14:25,681] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3c5f08e-5fd2-474b-9e46-464f5fedbaef/GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:14:38,085] [INFO] Task succeeded: Prodigal
[2023-06-29 20:14:38,086] [INFO] Task started: HMMsearch
[2023-06-29 20:14:38,086] [INFO] Running command: hmmsearch --tblout GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0fa29f2-9316-485f-98d3-1fda5e040add/dqc_reference/reference_markers.hmm GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:14:38,399] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:14:38,401] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc3c5f08e-5fd2-474b-9e46-464f5fedbaef/GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 20:14:38,444] [INFO] Query marker FASTA was written to GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 20:14:38,445] [INFO] Task started: Blastn
[2023-06-29 20:14:38,445] [INFO] Running command: blastn -query GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0fa29f2-9316-485f-98d3-1fda5e040add/dqc_reference/reference_markers.fasta -out GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:14:39,234] [INFO] Task succeeded: Blastn
[2023-06-29 20:14:39,238] [INFO] Selected 30 target genomes.
[2023-06-29 20:14:39,239] [INFO] Target genome list was writen to GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 20:14:39,240] [INFO] Task started: fastANI
[2023-06-29 20:14:39,240] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3c5f08e-5fd2-474b-9e46-464f5fedbaef/GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:15:02,947] [INFO] Task succeeded: fastANI
[2023-06-29 20:15:02,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0fa29f2-9316-485f-98d3-1fda5e040add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:15:02,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0fa29f2-9316-485f-98d3-1fda5e040add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:15:02,968] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:15:02,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:15:02,969] [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
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.4528	144	1210	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.2412	117	1210	95	below_threshold
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	76.0909	61	1210	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.0757	123	1210	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.025	206	1210	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.9805	205	1210	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.9204	176	1210	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.9139	205	1210	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	75.8815	58	1210	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.8469	176	1210	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8364	214	1210	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	75.8286	111	1210	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.805	135	1210	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.791	129	1210	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.7706	118	1210	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	75.7617	93	1210	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	75.7436	113	1210	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.7203	127	1210	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	75.6962	124	1210	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	75.6254	119	1210	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	75.617	138	1210	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	75.5853	132	1210	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.4787	106	1210	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	75.4432	77	1210	95	below_threshold
Sandarakinorhabdus cyanobacteriorum	strain=TH057	GCA_002251755.1	1981098	1981098	type	True	75.4233	52	1210	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	75.4196	152	1210	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	75.2746	62	1210	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	75.0936	72	1210	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	75.0705	62	1210	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:15:02,971] [INFO] DFAST Taxonomy check result was written to GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 20:15:02,972] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:15:02,972] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:15:02,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0fa29f2-9316-485f-98d3-1fda5e040add/dqc_reference/checkm_data
[2023-06-29 20:15:02,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:15:03,022] [INFO] Task started: CheckM
[2023-06-29 20:15:03,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 20:15:40,402] [INFO] Task succeeded: CheckM
[2023-06-29 20:15:40,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.82%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 20:15:40,426] [INFO] ===== Completeness check finished =====
[2023-06-29 20:15:40,426] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:15:40,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 20:15:40,427] [INFO] Task started: Blastn
[2023-06-29 20:15:40,427] [INFO] Running command: blastn -query GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0fa29f2-9316-485f-98d3-1fda5e040add/dqc_reference/reference_markers_gtdb.fasta -out GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:15:41,758] [INFO] Task succeeded: Blastn
[2023-06-29 20:15:41,763] [INFO] Selected 23 target genomes.
[2023-06-29 20:15:41,764] [INFO] Target genome list was writen to GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:15:41,767] [INFO] Task started: fastANI
[2023-06-29 20:15:41,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3c5f08e-5fd2-474b-9e46-464f5fedbaef/GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:16:00,536] [INFO] Task succeeded: fastANI
[2023-06-29 20:16:00,560] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:16:00,560] [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_002690215.1	s__GCA-2690215 sp002690215	99.4061	972	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__GCA-2690215	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016869515.1	s__VGDZ01 sp016869515	76.6066	185	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__VGDZ01;f__VGDZ01;g__VGDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781745.1	s__UBA1479 sp002781745	76.1724	127	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693905.1	s__2-12-FULL-67-15 sp009693905	76.1589	69	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	99.79	99.79	0.72	0.72	2	-
GCA_000518365.1	s__URHD0088 sp000518365	76.0371	149	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	76.0084	102	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006218045.1	s__Magnetospirillum sp006218045	75.9819	103	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.95	99.95	0.98	0.98	2	-
GCA_017305915.1	s__Reyranella sp017305915	75.8597	168	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197755.1	s__Ferrovibrio terrae	75.8286	111	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	75.8196	180	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	75.7834	104	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	75.7812	154	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828035.1	s__Nitrospirillum amazonense_A	75.7566	142	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356985.1	s__SMXQ01 sp004356985	75.7269	80	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__SMXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298965.1	s__Pinisolibacter sp002298965	75.7103	87	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	75.6859	163	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	75.6781	126	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_016629525.1	s__Kaistia sp016629525	75.6542	106	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333275.1	s__Nitrospirillum sp000333275	75.6426	131	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828045.1	s__Nitrospirillum amazonense_C	75.6326	137	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730165.1	s__Nitrospirillum amazonense	75.5563	159	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	97.38	95.62	0.93	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-29 20:16:00,562] [INFO] GTDB search result was written to GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 20:16:00,563] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:16:00,568] [INFO] DFAST_QC result json was written to GCA_937892245.1_ERR599062_bin.144_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 20:16:00,568] [INFO] DFAST_QC completed!
[2023-06-29 20:16:00,568] [INFO] Total running time: 0h1m36s