[2024-01-24 12:31:58,691] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d7d6371-d11d-4b96-ba4a-4ea4478a4a8e/dqc_reference
[2024-01-24 12:32:00,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:32:00,020] [INFO] Task started: Prodigal
[2024-01-24 12:32:00,020] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb919e28-9bf9-48ac-aa5a-cb2187c8d89a/GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/cds.fna -a GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:14,058] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:14,058] [INFO] Task started: HMMsearch
[2024-01-24 12:32:14,058] [INFO] Running command: hmmsearch --tblout GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d7d6371-d11d-4b96-ba4a-4ea4478a4a8e/dqc_reference/reference_markers.hmm GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:14,372] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:14,373] [INFO] Found 6/6 markers.
[2024-01-24 12:32:14,417] [INFO] Query marker FASTA was written to GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:32:14,418] [INFO] Task started: Blastn
[2024-01-24 12:32:14,418] [INFO] Running command: blastn -query GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d7d6371-d11d-4b96-ba4a-4ea4478a4a8e/dqc_reference/reference_markers.fasta -out GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:15,534] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:15,537] [INFO] Selected 14 target genomes.
[2024-01-24 12:32:15,538] [INFO] Target genome list was writen to GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:32:15,541] [INFO] Task started: fastANI
[2024-01-24 12:32:15,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb919e28-9bf9-48ac-aa5a-cb2187c8d89a/GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna.gz --refList GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:33,541] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:33,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d7d6371-d11d-4b96-ba4a-4ea4478a4a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:33,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d7d6371-d11d-4b96-ba4a-4ea4478a4a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:33,553] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:32:33,553] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:33,554] [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
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	100.0	1510	1513	95	conclusive
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	99.9161	1412	1513	95	conclusive
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	94.853	1214	1513	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	84.2194	1005	1513	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	84.1861	1026	1513	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	83.4154	902	1513	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	81.2051	666	1513	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.7442	678	1513	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.6983	672	1513	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	80.6003	849	1513	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	80.5718	828	1513	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	80.5694	799	1513	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.6364	541	1513	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.5764	637	1513	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:33,555] [INFO] DFAST Taxonomy check result was written to GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:32:33,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:33,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:33,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d7d6371-d11d-4b96-ba4a-4ea4478a4a8e/dqc_reference/checkm_data
[2024-01-24 12:32:33,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:33,605] [INFO] Task started: CheckM
[2024-01-24 12:32:33,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/checkm_input GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:33:57,892] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:57,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:57,917] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:57,918] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:57,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:33:57,919] [INFO] Task started: Blastn
[2024-01-24 12:33:57,919] [INFO] Running command: blastn -query GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d7d6371-d11d-4b96-ba4a-4ea4478a4a8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:00,229] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:00,234] [INFO] Selected 12 target genomes.
[2024-01-24 12:34:00,234] [INFO] Target genome list was writen to GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:34:00,250] [INFO] Task started: fastANI
[2024-01-24 12:34:00,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb919e28-9bf9-48ac-aa5a-cb2187c8d89a/GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna.gz --refList GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:34:17,571] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:17,586] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:34:17,586] [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
GCF_900156335.1	s__Sphaerotilus natans	100.0	1510	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_008329925.1	s__Sphaerotilus sulfidivorans	94.811	1240	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013294065.1	s__Sphaerotilus sp013294065	92.3202	1189	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410775.1	s__Sphaerotilus montanus	84.2147	1022	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003201595.1	s__Sphaerotilus hippei	83.3818	905	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013299175.1	s__Sphaerotilus sp013299175	83.1565	812	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019785.1	s__Leptothrix cholodnii	82.7897	895	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Leptothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216565.1	s__Leptothrix mobilis	82.1182	835	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Leptothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	81.4182	810	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_012927045.1	s__Azohydromonas caseinilytica	80.6219	821	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430725.1	s__Azohydromonas australica	80.5204	807	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	80.1491	752	1513	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:34:17,588] [INFO] GTDB search result was written to GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:34:17,588] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:34:17,592] [INFO] DFAST_QC result json was written to GCF_900156335.1_IMG-taxon_2681812894_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:34:17,592] [INFO] DFAST_QC completed!
[2024-01-24 12:34:17,592] [INFO] Total running time: 0h2m19s