[2024-01-25 19:34:21,021] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:21,026] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:21,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg461259ce-c518-44f7-ba01-9afb851a0b3f/dqc_reference
[2024-01-25 19:34:22,163] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:22,164] [INFO] Task started: Prodigal
[2024-01-25 19:34:22,164] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f767bb4-ee31-4874-9db8-eb98d4b80f6a/GCF_012940005.1_ASM1294000v1_genomic.fna.gz | prodigal -d GCF_012940005.1_ASM1294000v1_genomic.fna/cds.fna -a GCF_012940005.1_ASM1294000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:34:35,247] [INFO] Task succeeded: Prodigal
[2024-01-25 19:34:35,248] [INFO] Task started: HMMsearch
[2024-01-25 19:34:35,248] [INFO] Running command: hmmsearch --tblout GCF_012940005.1_ASM1294000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg461259ce-c518-44f7-ba01-9afb851a0b3f/dqc_reference/reference_markers.hmm GCF_012940005.1_ASM1294000v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:34:35,504] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:34:35,505] [INFO] Found 6/6 markers.
[2024-01-25 19:34:35,545] [INFO] Query marker FASTA was written to GCF_012940005.1_ASM1294000v1_genomic.fna/markers.fasta
[2024-01-25 19:34:35,546] [INFO] Task started: Blastn
[2024-01-25 19:34:35,546] [INFO] Running command: blastn -query GCF_012940005.1_ASM1294000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg461259ce-c518-44f7-ba01-9afb851a0b3f/dqc_reference/reference_markers.fasta -out GCF_012940005.1_ASM1294000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:36,225] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:36,227] [INFO] Selected 17 target genomes.
[2024-01-25 19:34:36,228] [INFO] Target genome list was writen to GCF_012940005.1_ASM1294000v1_genomic.fna/target_genomes.txt
[2024-01-25 19:34:36,232] [INFO] Task started: fastANI
[2024-01-25 19:34:36,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f767bb4-ee31-4874-9db8-eb98d4b80f6a/GCF_012940005.1_ASM1294000v1_genomic.fna.gz --refList GCF_012940005.1_ASM1294000v1_genomic.fna/target_genomes.txt --output GCF_012940005.1_ASM1294000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:48,789] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:48,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg461259ce-c518-44f7-ba01-9afb851a0b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:48,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg461259ce-c518-44f7-ba01-9afb851a0b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:48,809] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:34:48,809] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:34:48,809] [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
Candidatus Accumulibacter contiguus		GCA_012940005.1	2954381	2954381	type	True	100.0	1586	1592	95	conclusive
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	77.8654	343	1592	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	77.8546	343	1592	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.8114	301	1592	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	77.5391	265	1592	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	77.5389	295	1592	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	77.3046	244	1592	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	77.2765	251	1592	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	77.2409	250	1592	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	77.1302	286	1592	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	76.9205	243	1592	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.8035	211	1592	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	76.7733	213	1592	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	75.9112	91	1592	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	75.7458	144	1592	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	75.6528	122	1592	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	75.6157	128	1592	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:48,811] [INFO] DFAST Taxonomy check result was written to GCF_012940005.1_ASM1294000v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:48,811] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:48,811] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:48,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg461259ce-c518-44f7-ba01-9afb851a0b3f/dqc_reference/checkm_data
[2024-01-25 19:34:48,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:48,865] [INFO] Task started: CheckM
[2024-01-25 19:34:48,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012940005.1_ASM1294000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012940005.1_ASM1294000v1_genomic.fna/checkm_input GCF_012940005.1_ASM1294000v1_genomic.fna/checkm_result
[2024-01-25 19:35:31,291] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:31,294] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:31,314] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:31,314] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:31,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012940005.1_ASM1294000v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:31,316] [INFO] Task started: Blastn
[2024-01-25 19:35:31,316] [INFO] Running command: blastn -query GCF_012940005.1_ASM1294000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg461259ce-c518-44f7-ba01-9afb851a0b3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_012940005.1_ASM1294000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:32,425] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:32,428] [INFO] Selected 10 target genomes.
[2024-01-25 19:35:32,428] [INFO] Target genome list was writen to GCF_012940005.1_ASM1294000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:32,436] [INFO] Task started: fastANI
[2024-01-25 19:35:32,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f767bb4-ee31-4874-9db8-eb98d4b80f6a/GCF_012940005.1_ASM1294000v1_genomic.fna.gz --refList GCF_012940005.1_ASM1294000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012940005.1_ASM1294000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:43,900] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:43,907] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:43,908] [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_012940005.1	s__Accumulibacter phosphatis_H	100.0	1586	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.13	99.13	0.91	0.91	2	conclusive
GCA_002425405.1	s__Accumulibacter phosphatis_E	89.1328	944	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.65	99.65	0.90	0.90	2	-
GCF_005889575.1	s__Accumulibacter sp000584975	88.404	1026	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	98.95	98.61	0.89	0.84	7	-
GCA_016713625.1	s__Accumulibacter sp016713625	82.5561	847	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.10	99.10	0.76	0.76	2	-
GCA_016709675.1	s__Accumulibacter sp016709675	82.0537	801	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	98.87	98.87	0.92	0.92	2	-
GCA_017302435.1	s__Accumulibacter sp017302435	81.6144	803	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714935.1	s__Accumulibacter sp016714935	81.4668	767	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	98.82	98.60	0.85	0.81	4	-
GCF_000024165.1	s__Accumulibacter phosphatis_C	81.2506	805	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	98.52	96.04	0.92	0.86	4	-
GCF_900089955.1	s__Accumulibacter aalborgensis	81.0205	769	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012939955.1	s__Accumulibacter phosphatis_G	79.5889	613	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	98.73	98.73	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:43,910] [INFO] GTDB search result was written to GCF_012940005.1_ASM1294000v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:43,911] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:43,914] [INFO] DFAST_QC result json was written to GCF_012940005.1_ASM1294000v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:43,914] [INFO] DFAST_QC completed!
[2024-01-25 19:35:43,914] [INFO] Total running time: 0h1m23s