[2023-03-17 22:46:02,534] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:46:02,534] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:46:02,534] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb8fe237-fd5f-4bd6-a13f-5d9b74ed67da/dqc_reference
[2023-03-17 22:46:03,671] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:46:03,672] [INFO] Task started: Prodigal
[2023-03-17 22:46:03,672] [INFO] Running command: cat /var/lib/cwl/stgd75e19eb-6819-4e01-b9f5-4bb5e4662c55/OceanDNA-b33431.fa | prodigal -d OceanDNA-b33431/cds.fna -a OceanDNA-b33431/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:46:15,478] [INFO] Task succeeded: Prodigal
[2023-03-17 22:46:15,479] [INFO] Task started: HMMsearch
[2023-03-17 22:46:15,479] [INFO] Running command: hmmsearch --tblout OceanDNA-b33431/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb8fe237-fd5f-4bd6-a13f-5d9b74ed67da/dqc_reference/reference_markers.hmm OceanDNA-b33431/protein.faa > /dev/null
[2023-03-17 22:46:15,659] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:46:15,659] [INFO] Found 6/6 markers.
[2023-03-17 22:46:15,673] [INFO] Query marker FASTA was written to OceanDNA-b33431/markers.fasta
[2023-03-17 22:46:15,674] [INFO] Task started: Blastn
[2023-03-17 22:46:15,674] [INFO] Running command: blastn -query OceanDNA-b33431/markers.fasta -db /var/lib/cwl/stgfb8fe237-fd5f-4bd6-a13f-5d9b74ed67da/dqc_reference/reference_markers.fasta -out OceanDNA-b33431/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:46:16,324] [INFO] Task succeeded: Blastn
[2023-03-17 22:46:16,325] [INFO] Selected 29 target genomes.
[2023-03-17 22:46:16,325] [INFO] Target genome list was writen to OceanDNA-b33431/target_genomes.txt
[2023-03-17 22:46:16,345] [INFO] Task started: fastANI
[2023-03-17 22:46:16,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgd75e19eb-6819-4e01-b9f5-4bb5e4662c55/OceanDNA-b33431.fa --refList OceanDNA-b33431/target_genomes.txt --output OceanDNA-b33431/fastani_result.tsv --threads 1
[2023-03-17 22:46:34,254] [INFO] Task succeeded: fastANI
[2023-03-17 22:46:34,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb8fe237-fd5f-4bd6-a13f-5d9b74ed67da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:46:34,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb8fe237-fd5f-4bd6-a13f-5d9b74ed67da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:46:34,269] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:46:34,269] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 22:46:34,269] [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
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	77.2761	155	552	95	below_threshold
Serpentinimonas raichei	strain=A1	GCA_000828895.1	1458425	1458425	type	True	77.1309	152	552	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	77.1282	167	552	95	below_threshold
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	77.0982	169	552	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	77.0601	180	552	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	76.8155	166	552	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	76.6945	136	552	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	76.651	174	552	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	76.6456	127	552	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	76.636	127	552	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	76.6249	154	552	95	below_threshold
Verminephrobacter eiseniae	strain=EF01-2	GCA_000015565.1	364317	364317	type	True	76.6134	122	552	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	76.6095	152	552	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	76.6007	153	552	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	76.5812	140	552	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	76.517	148	552	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	76.4433	117	552	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	76.3762	140	552	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	76.332	128	552	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	76.3121	71	552	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	76.3004	141	552	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	76.2876	143	552	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	76.268	127	552	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	76.2236	87	552	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	76.2209	87	552	95	below_threshold
Comamonas kerstersii	strain=CCUG 15333	GCA_008801935.1	225992	225992	type	True	76.1154	76	552	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	76.0956	103	552	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:46:34,269] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33431/tc_result.tsv
[2023-03-17 22:46:34,269] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:46:34,270] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:46:34,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb8fe237-fd5f-4bd6-a13f-5d9b74ed67da/dqc_reference/checkm_data
[2023-03-17 22:46:34,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:46:34,371] [INFO] Task started: CheckM
[2023-03-17 22:46:34,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33431/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33431/checkm_input OceanDNA-b33431/checkm_result
[2023-03-17 22:47:07,067] [INFO] Task succeeded: CheckM
[2023-03-17 22:47:07,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:47:07,071] [INFO] ===== Completeness check finished =====
[2023-03-17 22:47:07,071] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:47:07,071] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33431/markers.fasta)
[2023-03-17 22:47:07,072] [INFO] Task started: Blastn
[2023-03-17 22:47:07,072] [INFO] Running command: blastn -query OceanDNA-b33431/markers.fasta -db /var/lib/cwl/stgfb8fe237-fd5f-4bd6-a13f-5d9b74ed67da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33431/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:47:08,145] [INFO] Task succeeded: Blastn
[2023-03-17 22:47:08,146] [INFO] Selected 29 target genomes.
[2023-03-17 22:47:08,146] [INFO] Target genome list was writen to OceanDNA-b33431/target_genomes_gtdb.txt
[2023-03-17 22:47:08,168] [INFO] Task started: fastANI
[2023-03-17 22:47:08,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgd75e19eb-6819-4e01-b9f5-4bb5e4662c55/OceanDNA-b33431.fa --refList OceanDNA-b33431/target_genomes_gtdb.txt --output OceanDNA-b33431/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:47:24,273] [INFO] Task succeeded: fastANI
[2023-03-17 22:47:24,289] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:47:24,290] [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_009921245.1	s__RFXW01 sp009921245	81.7332	399	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837135.1	s__Macromonas bipunctata	77.1916	141	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Macromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837145.1	s__BK-30 sp002837145	77.0494	163	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	77.0003	158	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391745.1	s__Hydrogenophaga sp011391745	76.9953	121	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823635.1	s__UBA2334 sp013823635	76.8475	163	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454975.1	s__Hylemonella sp002454975	76.8097	151	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363315.1	s__Tepidicella xavieri	76.7884	152	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391495.1	s__Hydrogenophaga sp011391495	76.7743	120	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693755.1	s__Tibeticola sp013693755	76.7068	154	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCF_010020825.1	s__Giesbergeria sp010020825	76.6515	133	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.40	98.40	0.98	0.98	2	-
GCF_001571225.1	s__Hydrogenophaga palleronii	76.6392	153	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903960915.1	s__Rhodoferax sp903960915	76.6371	147	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.23	97.99	0.89	0.81	4	-
GCA_903832625.1	s__Limnohabitans sp903832625	76.6036	124	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	97.24	97.19	0.90	0.89	4	-
GCF_004341365.1	s__Giesbergeria metamorpha	76.6007	153	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.27	98.54	0.92	0.85	3	-
GCA_016192425.1	s__Giesbergeria sp016192425	76.5493	134	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907163135.1	s__Brachymonas denitrificans_A	76.545	89	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004322085.1	s__Rhodoferax_A sp004322085	76.5031	81	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083775.1	s__Rhodoferax ferrireducens_A	76.4893	115	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852545.1	s__Acidovorax sp003852545	76.3857	166	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218755.1	s__Acidovorax sp019218755	76.3606	137	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
GCA_018384835.1	s__Comamonas sp018384835	76.2962	67	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428875.1	s__Xylophilus sp016428875	76.2471	152	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217575.1	s__Xylophilus ampelinus	76.2413	86	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801935.1	s__Comamonas kerstersii	76.1154	76	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.88	98.82	0.91	0.88	10	-
GCF_008801845.1	s__Ideonella dechloratans	76.1005	101	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421705.1	s__Xylophilus sp001421705	76.0903	96	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333615.1	s__Ideonella sp000333615	75.8867	82	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204525.1	s__Paucibacter_A oligotrophus	75.519	90	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:47:24,290] [INFO] GTDB search result was written to OceanDNA-b33431/result_gtdb.tsv
[2023-03-17 22:47:24,290] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:47:24,293] [INFO] DFAST_QC result json was written to OceanDNA-b33431/dqc_result.json
[2023-03-17 22:47:24,293] [INFO] DFAST_QC completed!
[2023-03-17 22:47:24,293] [INFO] Total running time: 0h1m22s