[2023-06-30 03:56:18,725] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:56:18,732] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:56:18,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg68efcaac-c549-4a44-83f7-d6242ad74a53/dqc_reference
[2023-06-30 03:56:19,980] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:56:19,981] [INFO] Task started: Prodigal
[2023-06-30 03:56:19,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c8f8f9a-46e1-4d67-996c-b7c11afa176b/GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna.gz | prodigal -d GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/cds.fna -a GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:56:29,195] [INFO] Task succeeded: Prodigal
[2023-06-30 03:56:29,196] [INFO] Task started: HMMsearch
[2023-06-30 03:56:29,196] [INFO] Running command: hmmsearch --tblout GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68efcaac-c549-4a44-83f7-d6242ad74a53/dqc_reference/reference_markers.hmm GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:56:29,451] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:56:29,452] [INFO] Found 6/6 markers.
[2023-06-30 03:56:29,483] [INFO] Query marker FASTA was written to GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/markers.fasta
[2023-06-30 03:56:29,483] [INFO] Task started: Blastn
[2023-06-30 03:56:29,484] [INFO] Running command: blastn -query GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/markers.fasta -db /var/lib/cwl/stg68efcaac-c549-4a44-83f7-d6242ad74a53/dqc_reference/reference_markers.fasta -out GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:56:30,448] [INFO] Task succeeded: Blastn
[2023-06-30 03:56:30,452] [INFO] Selected 19 target genomes.
[2023-06-30 03:56:30,452] [INFO] Target genome list was writen to GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/target_genomes.txt
[2023-06-30 03:56:30,453] [INFO] Task started: fastANI
[2023-06-30 03:56:30,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c8f8f9a-46e1-4d67-996c-b7c11afa176b/GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna.gz --refList GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/target_genomes.txt --output GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:56:44,547] [INFO] Task succeeded: fastANI
[2023-06-30 03:56:44,548] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68efcaac-c549-4a44-83f7-d6242ad74a53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:56:44,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68efcaac-c549-4a44-83f7-d6242ad74a53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:56:44,568] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:56:44,568] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:56:44,569] [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
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	80.0104	405	979	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	79.9529	402	979	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.3673	311	979	95	below_threshold
Georgfuchsia toluolica	strain=G5G6	GCA_907163265.1	424218	424218	type	True	78.3669	277	979	95	below_threshold
Sterolibacterium denitrificans	strain=DSM 13999	GCA_001586935.1	157592	157592	type	True	78.3228	115	979	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	78.2408	291	979	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	78.1752	284	979	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	77.9804	300	979	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	77.9307	273	979	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	77.8111	260	979	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	77.6412	279	979	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	77.5855	288	979	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	77.5515	243	979	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	77.5422	300	979	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.5041	214	979	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.1437	178	979	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	76.9272	191	979	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	76.7114	214	979	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.6441	189	979	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:56:44,571] [INFO] DFAST Taxonomy check result was written to GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/tc_result.tsv
[2023-06-30 03:56:44,572] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:56:44,572] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:56:44,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68efcaac-c549-4a44-83f7-d6242ad74a53/dqc_reference/checkm_data
[2023-06-30 03:56:44,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:56:44,615] [INFO] Task started: CheckM
[2023-06-30 03:56:44,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/checkm_input GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/checkm_result
[2023-06-30 03:57:16,537] [INFO] Task succeeded: CheckM
[2023-06-30 03:57:16,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:57:16,564] [INFO] ===== Completeness check finished =====
[2023-06-30 03:57:16,564] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:57:16,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/markers.fasta)
[2023-06-30 03:57:16,565] [INFO] Task started: Blastn
[2023-06-30 03:57:16,565] [INFO] Running command: blastn -query GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/markers.fasta -db /var/lib/cwl/stg68efcaac-c549-4a44-83f7-d6242ad74a53/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:57:18,465] [INFO] Task succeeded: Blastn
[2023-06-30 03:57:18,470] [INFO] Selected 11 target genomes.
[2023-06-30 03:57:18,470] [INFO] Target genome list was writen to GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:57:18,471] [INFO] Task started: fastANI
[2023-06-30 03:57:18,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c8f8f9a-46e1-4d67-996c-b7c11afa176b/GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna.gz --refList GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/target_genomes_gtdb.txt --output GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:57:27,001] [INFO] Task succeeded: fastANI
[2023-06-30 03:57:27,014] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:57:27,014] [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_903848955.1	s__Sulfuritalea sp903848955	99.5742	894	979	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.61	99.42	0.91	0.84	24	conclusive
GCA_006218025.1	s__Sulfuritalea sp006218025	84.1338	634	979	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000828635.1	s__Sulfuritalea hydrogenivorans	83.788	626	979	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192435.1	s__Sulfuritalea sp016192435	83.4141	513	979	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708585.1	s__Sulfuritalea sp016708585	83.2608	574	979	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001828935.1	s__Sulfuritalea sp001828935	82.9641	590	979	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903933395.1	s__Sulfuritalea sp903933395	82.8796	473	979	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.21	99.21	0.82	0.82	2	-
GCA_016712985.1	s__Sulfuritalea sp016712985	82.8181	611	979	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	97.95	97.95	0.80	0.80	2	-
GCA_012026675.1	s__Sulfuritalea sp012026675	82.4378	504	979	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235805.1	s__Sulfuritalea sp016235805	81.9758	498	979	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903932755.1	s__Sulfuritalea sp903932755	81.2648	324	979	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	98.78	98.78	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2023-06-30 03:57:27,016] [INFO] GTDB search result was written to GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/result_gtdb.tsv
[2023-06-30 03:57:27,016] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:57:27,020] [INFO] DFAST_QC result json was written to GCA_903830375.1_freshwater_MAG_---_LJ-5-9m_bin-0354_genomic.fna/dqc_result.json
[2023-06-30 03:57:27,020] [INFO] DFAST_QC completed!
[2023-06-30 03:57:27,020] [INFO] Total running time: 0h1m8s