[2023-03-17 00:02:20,736] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:02:20,736] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:02:20,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg43680727-0eae-46fb-9321-a2746c4f80a1/dqc_reference
[2023-03-17 00:02:21,843] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:02:21,845] [INFO] Task started: Prodigal
[2023-03-17 00:02:21,845] [INFO] Running command: cat /var/lib/cwl/stg2d5d396a-1996-4355-ba58-248badb987c8/OceanDNA-b33515.fa | prodigal -d OceanDNA-b33515/cds.fna -a OceanDNA-b33515/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:02:37,610] [INFO] Task succeeded: Prodigal
[2023-03-17 00:02:37,610] [INFO] Task started: HMMsearch
[2023-03-17 00:02:37,610] [INFO] Running command: hmmsearch --tblout OceanDNA-b33515/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43680727-0eae-46fb-9321-a2746c4f80a1/dqc_reference/reference_markers.hmm OceanDNA-b33515/protein.faa > /dev/null
[2023-03-17 00:02:37,808] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:02:37,809] [INFO] Found 6/6 markers.
[2023-03-17 00:02:37,826] [INFO] Query marker FASTA was written to OceanDNA-b33515/markers.fasta
[2023-03-17 00:02:37,826] [INFO] Task started: Blastn
[2023-03-17 00:02:37,826] [INFO] Running command: blastn -query OceanDNA-b33515/markers.fasta -db /var/lib/cwl/stg43680727-0eae-46fb-9321-a2746c4f80a1/dqc_reference/reference_markers.fasta -out OceanDNA-b33515/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:02:38,451] [INFO] Task succeeded: Blastn
[2023-03-17 00:02:38,452] [INFO] Selected 31 target genomes.
[2023-03-17 00:02:38,452] [INFO] Target genome list was writen to OceanDNA-b33515/target_genomes.txt
[2023-03-17 00:02:38,625] [INFO] Task started: fastANI
[2023-03-17 00:02:38,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d5d396a-1996-4355-ba58-248badb987c8/OceanDNA-b33515.fa --refList OceanDNA-b33515/target_genomes.txt --output OceanDNA-b33515/fastani_result.tsv --threads 1
[2023-03-17 00:02:57,404] [INFO] Task succeeded: fastANI
[2023-03-17 00:02:57,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43680727-0eae-46fb-9321-a2746c4f80a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:02:57,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43680727-0eae-46fb-9321-a2746c4f80a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:02:57,419] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:02:57,419] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:02:57,419] [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
Rhodoferax fermentans	strain=DSM 10138	GCA_016583655.1	28066	28066	type	True	77.3409	187	769	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	77.3351	188	769	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	77.2774	165	769	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	77.2591	164	769	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	77.0486	158	769	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	77.0106	106	769	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	76.9244	119	769	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	76.9061	132	769	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	76.8498	127	769	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	76.8237	100	769	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	76.8139	113	769	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	76.7791	123	769	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	76.7763	135	769	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	76.7202	119	769	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	76.6718	121	769	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	76.6546	123	769	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	76.6272	122	769	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	76.615	92	769	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	76.5066	112	769	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	76.4781	83	769	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	76.3435	106	769	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	76.3306	95	769	95	below_threshold
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	76.2527	84	769	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	76.2249	87	769	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	76.1946	87	769	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	76.1933	99	769	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	76.1438	94	769	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	76.0626	90	769	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:02:57,420] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33515/tc_result.tsv
[2023-03-17 00:02:57,420] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:02:57,420] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:02:57,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43680727-0eae-46fb-9321-a2746c4f80a1/dqc_reference/checkm_data
[2023-03-17 00:02:57,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:02:57,575] [INFO] Task started: CheckM
[2023-03-17 00:02:57,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33515/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33515/checkm_input OceanDNA-b33515/checkm_result
[2023-03-17 00:03:40,644] [INFO] Task succeeded: CheckM
[2023-03-17 00:03:40,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.47%
Contamintation: 6.02%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-03-17 00:03:40,726] [INFO] ===== Completeness check finished =====
[2023-03-17 00:03:40,726] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:03:40,726] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33515/markers.fasta)
[2023-03-17 00:03:40,727] [INFO] Task started: Blastn
[2023-03-17 00:03:40,727] [INFO] Running command: blastn -query OceanDNA-b33515/markers.fasta -db /var/lib/cwl/stg43680727-0eae-46fb-9321-a2746c4f80a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33515/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:03:41,825] [INFO] Task succeeded: Blastn
[2023-03-17 00:03:41,826] [INFO] Selected 26 target genomes.
[2023-03-17 00:03:41,826] [INFO] Target genome list was writen to OceanDNA-b33515/target_genomes_gtdb.txt
[2023-03-17 00:03:42,059] [INFO] Task started: fastANI
[2023-03-17 00:03:42,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d5d396a-1996-4355-ba58-248badb987c8/OceanDNA-b33515.fa --refList OceanDNA-b33515/target_genomes_gtdb.txt --output OceanDNA-b33515/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:03:59,639] [INFO] Task succeeded: fastANI
[2023-03-17 00:03:59,654] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:03:59,654] [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_011391645.1	s__Rhodoferax sp011391645	77.5573	165	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083775.1	s__Rhodoferax ferrireducens_A	77.5415	181	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859475.1	s__Rhodoferax sp014859475	77.5372	160	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416775.1	s__Rhodoferax sp013416775	77.4752	193	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842265.1	s__Rhodoferax sp002842265	77.4461	166	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001771065.1	s__Rhodoferax sp001771065	77.4344	175	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018619435.1	s__Rhodoferax sp018619435	77.4164	185	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903905735.1	s__Rhodoferax sp903905735	77.3384	174	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008080595.1	s__Rhodoferax sp008080595	77.2921	182	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001938565.1	s__Rhodoferax antarcticus	77.2598	166	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.96	99.96	0.95	0.95	2	-
GCA_002454975.1	s__Hylemonella sp002454975	77.2115	145	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002789915.1	s__Rhodoferax sp002789915	77.0846	151	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.63	99.52	0.89	0.89	3	-
GCF_000013605.1	s__Rhodoferax ferrireducens	77.0783	157	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	95.18	95.18	0.88	0.88	2	-
GCA_017880985.1	s__Rhodoferax sp017880985	76.9739	87	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719055.1	s__Rhodoferax sp016719055	76.945	155	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013791765.1	s__Rhodoferax sp013791765	76.9297	147	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.97	99.92	0.98	0.96	7	-
GCA_010365055.1	s__Rhodoferax sp010365055	76.9128	154	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381265.1	s__Curvibacter lanceolatus	76.8498	127	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.6079	99.38	99.38	0.94	0.94	2	-
GCA_003987795.1	s__Curvibacter sp003987795	76.8233	94	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518645.1	s__Curvibacter gracilis	76.7763	135	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.6079	N/A	N/A	N/A	N/A	1	-
GCA_016718405.1	s__Rhodoferax sp016718405	76.7674	126	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.26	98.26	0.90	0.90	2	-
GCA_016703945.1	s__Rhodoferax sp016703945	76.7326	127	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018063565.1	s__Rhodoferax sp018063565	76.7059	137	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870955.1	s__Rhodoferax sp903870955	76.6982	68	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.51	98.51	0.73	0.73	2	-
GCF_003063545.1	s__Limnohabitans sp003063545	76.6768	112	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853895.1	s__Rhodoferax sp903853895	76.6629	114	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.86	99.86	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:03:59,656] [INFO] GTDB search result was written to OceanDNA-b33515/result_gtdb.tsv
[2023-03-17 00:03:59,656] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:03:59,659] [INFO] DFAST_QC result json was written to OceanDNA-b33515/dqc_result.json
[2023-03-17 00:03:59,659] [INFO] DFAST_QC completed!
[2023-03-17 00:03:59,659] [INFO] Total running time: 0h1m39s