[2023-06-19 11:23:19,041] [INFO] DFAST_QC pipeline started.
[2023-06-19 11:23:19,043] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 11:23:19,043] [INFO] DQC Reference Directory: /var/lib/cwl/stgb31204bc-3180-4e4f-a73f-f731b89b2788/dqc_reference
[2023-06-19 11:23:20,293] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 11:23:20,293] [INFO] Task started: Prodigal
[2023-06-19 11:23:20,294] [INFO] Running command: gunzip -c /var/lib/cwl/stge50c7b17-a3ad-475a-8a64-ea8609b6d106/GCA_018882925.1_ASM1888292v1_genomic.fna.gz | prodigal -d GCA_018882925.1_ASM1888292v1_genomic.fna/cds.fna -a GCA_018882925.1_ASM1888292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 11:23:30,218] [INFO] Task succeeded: Prodigal
[2023-06-19 11:23:30,218] [INFO] Task started: HMMsearch
[2023-06-19 11:23:30,218] [INFO] Running command: hmmsearch --tblout GCA_018882925.1_ASM1888292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb31204bc-3180-4e4f-a73f-f731b89b2788/dqc_reference/reference_markers.hmm GCA_018882925.1_ASM1888292v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 11:23:30,562] [INFO] Task succeeded: HMMsearch
[2023-06-19 11:23:30,564] [INFO] Found 6/6 markers.
[2023-06-19 11:23:30,601] [INFO] Query marker FASTA was written to GCA_018882925.1_ASM1888292v1_genomic.fna/markers.fasta
[2023-06-19 11:23:30,601] [INFO] Task started: Blastn
[2023-06-19 11:23:30,601] [INFO] Running command: blastn -query GCA_018882925.1_ASM1888292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb31204bc-3180-4e4f-a73f-f731b89b2788/dqc_reference/reference_markers.fasta -out GCA_018882925.1_ASM1888292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:23:31,496] [INFO] Task succeeded: Blastn
[2023-06-19 11:23:31,499] [INFO] Selected 24 target genomes.
[2023-06-19 11:23:31,500] [INFO] Target genome list was writen to GCA_018882925.1_ASM1888292v1_genomic.fna/target_genomes.txt
[2023-06-19 11:23:31,502] [INFO] Task started: fastANI
[2023-06-19 11:23:31,502] [INFO] Running command: fastANI --query /var/lib/cwl/stge50c7b17-a3ad-475a-8a64-ea8609b6d106/GCA_018882925.1_ASM1888292v1_genomic.fna.gz --refList GCA_018882925.1_ASM1888292v1_genomic.fna/target_genomes.txt --output GCA_018882925.1_ASM1888292v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 11:23:50,276] [INFO] Task succeeded: fastANI
[2023-06-19 11:23:50,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb31204bc-3180-4e4f-a73f-f731b89b2788/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 11:23:50,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb31204bc-3180-4e4f-a73f-f731b89b2788/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 11:23:50,301] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 11:23:50,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 11:23:50,302] [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
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	81.7871	603	1086	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	81.7462	581	1086	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	81.6066	658	1086	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	81.4907	649	1086	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.4741	290	1086	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.4637	332	1086	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	78.4366	331	1086	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	78.1264	262	1086	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	78.1006	215	1086	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.8933	285	1086	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	77.8316	246	1086	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	77.7886	274	1086	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	76.9911	174	1086	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.9544	169	1086	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	76.8981	140	1086	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	76.8958	184	1086	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	76.8669	182	1086	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	76.8379	176	1086	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	76.6596	166	1086	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	76.5228	153	1086	95	below_threshold
Trinickia soli	strain=GP25-8	GCA_002879855.1	380675	380675	type	True	76.4304	83	1086	95	below_threshold
Trinickia soli	strain=LMG 24076	GCA_902859815.1	380675	380675	type	True	76.3445	81	1086	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 11:23:50,307] [INFO] DFAST Taxonomy check result was written to GCA_018882925.1_ASM1888292v1_genomic.fna/tc_result.tsv
[2023-06-19 11:23:50,307] [INFO] ===== Taxonomy check completed =====
[2023-06-19 11:23:50,308] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 11:23:50,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb31204bc-3180-4e4f-a73f-f731b89b2788/dqc_reference/checkm_data
[2023-06-19 11:23:50,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 11:23:50,345] [INFO] Task started: CheckM
[2023-06-19 11:23:50,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018882925.1_ASM1888292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018882925.1_ASM1888292v1_genomic.fna/checkm_input GCA_018882925.1_ASM1888292v1_genomic.fna/checkm_result
[2023-06-19 11:24:23,995] [INFO] Task succeeded: CheckM
[2023-06-19 11:24:23,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 11:24:24,021] [INFO] ===== Completeness check finished =====
[2023-06-19 11:24:24,021] [INFO] ===== Start GTDB Search =====
[2023-06-19 11:24:24,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018882925.1_ASM1888292v1_genomic.fna/markers.fasta)
[2023-06-19 11:24:24,022] [INFO] Task started: Blastn
[2023-06-19 11:24:24,022] [INFO] Running command: blastn -query GCA_018882925.1_ASM1888292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb31204bc-3180-4e4f-a73f-f731b89b2788/dqc_reference/reference_markers_gtdb.fasta -out GCA_018882925.1_ASM1888292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:24:25,421] [INFO] Task succeeded: Blastn
[2023-06-19 11:24:25,426] [INFO] Selected 21 target genomes.
[2023-06-19 11:24:25,426] [INFO] Target genome list was writen to GCA_018882925.1_ASM1888292v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 11:24:25,437] [INFO] Task started: fastANI
[2023-06-19 11:24:25,437] [INFO] Running command: fastANI --query /var/lib/cwl/stge50c7b17-a3ad-475a-8a64-ea8609b6d106/GCA_018882925.1_ASM1888292v1_genomic.fna.gz --refList GCA_018882925.1_ASM1888292v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018882925.1_ASM1888292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 11:24:41,054] [INFO] Task succeeded: fastANI
[2023-06-19 11:24:41,075] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 11:24:41,076] [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_004379165.1	s__Azonexus sp004379165	99.9215	957	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	99.94	99.94	0.95	0.95	2	conclusive
GCF_009469615.1	s__Azonexus sp009469615	82.1308	650	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519045.1	s__Azonexus agitatus	81.9979	621	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.62	98.62	0.86	0.86	2	-
GCF_008711155.1	s__Azonexus sp008711155	81.9044	605	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.59	97.59	0.92	0.92	2	-
GCF_003634965.1	s__Azonexus fungiphilus	81.8373	601	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.36	98.36	0.85	0.85	2	-
GCF_000429605.1	s__Azonexus hydrophilus	81.7629	580	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.24	97.24	0.86	0.86	2	-
GCA_002470165.1	s__Azonexus sp002470165	81.7167	409	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933675.1	s__Azonexus sp008933675	81.6817	572	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001551835.1	s__Azonexus denitrificans	81.6161	656	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469585.1	s__Azonexus sp009469585	81.6158	637	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983615.1	s__Azonexus sp017983615	81.4583	563	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956855.1	s__Azonexus hydrophilus_A	81.4305	606	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848965.1	s__Azonexus aromaticus_B	81.2951	586	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425245.1	s__Azonexus sp002425245	81.2804	504	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840765.1	s__Azonexus sp002840765	81.2362	616	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275485.1	s__Azonexus sp012275485	80.827	617	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345845.1	s__Azonexus sp002345845	80.7385	587	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720065.1	s__SSSZ01 sp016720065	79.1863	374	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__SSSZ01	95.0	99.85	99.82	0.99	0.97	4	-
GCA_009777925.1	s__Azovibrio sp009777925	76.5181	57	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879855.1	s__Trinickia soli	76.4304	83	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	99.68	99.37	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-19 11:24:41,078] [INFO] GTDB search result was written to GCA_018882925.1_ASM1888292v1_genomic.fna/result_gtdb.tsv
[2023-06-19 11:24:41,079] [INFO] ===== GTDB Search completed =====
[2023-06-19 11:24:41,084] [INFO] DFAST_QC result json was written to GCA_018882925.1_ASM1888292v1_genomic.fna/dqc_result.json
[2023-06-19 11:24:41,084] [INFO] DFAST_QC completed!
[2023-06-19 11:24:41,084] [INFO] Total running time: 0h1m22s