[2023-06-29 00:18:48,379] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:18:48,382] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:18:48,383] [INFO] DQC Reference Directory: /var/lib/cwl/stge2ccab69-197b-4f9c-a478-be3ba1821c2a/dqc_reference
[2023-06-29 00:18:49,577] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:18:49,579] [INFO] Task started: Prodigal
[2023-06-29 00:18:49,579] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a3593ab-f0c2-4177-929d-c1aaa6aeada8/GCA_019310365.1_ASM1931036v1_genomic.fna.gz | prodigal -d GCA_019310365.1_ASM1931036v1_genomic.fna/cds.fna -a GCA_019310365.1_ASM1931036v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:18:58,659] [INFO] Task succeeded: Prodigal
[2023-06-29 00:18:58,659] [INFO] Task started: HMMsearch
[2023-06-29 00:18:58,659] [INFO] Running command: hmmsearch --tblout GCA_019310365.1_ASM1931036v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2ccab69-197b-4f9c-a478-be3ba1821c2a/dqc_reference/reference_markers.hmm GCA_019310365.1_ASM1931036v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:18:58,869] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:18:58,870] [INFO] Found 6/6 markers.
[2023-06-29 00:18:58,905] [INFO] Query marker FASTA was written to GCA_019310365.1_ASM1931036v1_genomic.fna/markers.fasta
[2023-06-29 00:18:58,906] [INFO] Task started: Blastn
[2023-06-29 00:18:58,906] [INFO] Running command: blastn -query GCA_019310365.1_ASM1931036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2ccab69-197b-4f9c-a478-be3ba1821c2a/dqc_reference/reference_markers.fasta -out GCA_019310365.1_ASM1931036v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:18:59,682] [INFO] Task succeeded: Blastn
[2023-06-29 00:18:59,685] [INFO] Selected 29 target genomes.
[2023-06-29 00:18:59,686] [INFO] Target genome list was writen to GCA_019310365.1_ASM1931036v1_genomic.fna/target_genomes.txt
[2023-06-29 00:18:59,690] [INFO] Task started: fastANI
[2023-06-29 00:18:59,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a3593ab-f0c2-4177-929d-c1aaa6aeada8/GCA_019310365.1_ASM1931036v1_genomic.fna.gz --refList GCA_019310365.1_ASM1931036v1_genomic.fna/target_genomes.txt --output GCA_019310365.1_ASM1931036v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:19:23,609] [INFO] Task succeeded: fastANI
[2023-06-29 00:19:23,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2ccab69-197b-4f9c-a478-be3ba1821c2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:19:23,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2ccab69-197b-4f9c-a478-be3ba1821c2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:19:23,629] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:19:23,629] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:19:23,630] [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
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	75.2332	61	1170	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	75.1721	120	1170	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	75.0972	89	1170	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	75.0878	59	1170	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	75.0796	60	1170	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	75.0497	114	1170	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	75.0149	121	1170	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	75.0115	122	1170	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	75.008	122	1170	95	below_threshold
Aeromicrobium chenweiae	strain=592	GCA_003065605.1	2079793	2079793	type	True	74.9993	100	1170	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	74.9752	56	1170	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	74.974	84	1170	95	below_threshold
Aeromicrobium yanjiei	strain=MF47	GCA_009649075.1	2662028	2662028	type	True	74.9411	93	1170	95	below_threshold
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	74.9393	138	1170	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	74.9242	138	1170	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.8931	188	1170	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	74.885	121	1170	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.8655	130	1170	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.8455	233	1170	95	below_threshold
Burkholderia multivorans	strain=ATCC BAA-247	GCA_000959525.1	87883	87883	type	True	74.8038	159	1170	95	below_threshold
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	74.7966	111	1170	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	74.7468	172	1170	95	below_threshold
Halorubrum halophilum	strain=B8	GCA_000739595.1	413816	413816	type	True	74.6374	68	1170	95	below_threshold
Halorubrum coriense	strain=DSM 10284	GCA_000337035.1	64713	64713	type	True	74.6323	81	1170	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:19:23,632] [INFO] DFAST Taxonomy check result was written to GCA_019310365.1_ASM1931036v1_genomic.fna/tc_result.tsv
[2023-06-29 00:19:23,633] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:19:23,633] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:19:23,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2ccab69-197b-4f9c-a478-be3ba1821c2a/dqc_reference/checkm_data
[2023-06-29 00:19:23,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:19:23,674] [INFO] Task started: CheckM
[2023-06-29 00:19:23,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310365.1_ASM1931036v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310365.1_ASM1931036v1_genomic.fna/checkm_input GCA_019310365.1_ASM1931036v1_genomic.fna/checkm_result
[2023-06-29 00:19:53,192] [INFO] Task succeeded: CheckM
[2023-06-29 00:19:53,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 00:19:53,214] [INFO] ===== Completeness check finished =====
[2023-06-29 00:19:53,215] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:19:53,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310365.1_ASM1931036v1_genomic.fna/markers.fasta)
[2023-06-29 00:19:53,215] [INFO] Task started: Blastn
[2023-06-29 00:19:53,215] [INFO] Running command: blastn -query GCA_019310365.1_ASM1931036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2ccab69-197b-4f9c-a478-be3ba1821c2a/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310365.1_ASM1931036v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:19:54,586] [INFO] Task succeeded: Blastn
[2023-06-29 00:19:54,589] [INFO] Selected 25 target genomes.
[2023-06-29 00:19:54,589] [INFO] Target genome list was writen to GCA_019310365.1_ASM1931036v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:19:54,608] [INFO] Task started: fastANI
[2023-06-29 00:19:54,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a3593ab-f0c2-4177-929d-c1aaa6aeada8/GCA_019310365.1_ASM1931036v1_genomic.fna.gz --refList GCA_019310365.1_ASM1931036v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310365.1_ASM1931036v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:20:12,503] [INFO] Task succeeded: fastANI
[2023-06-29 00:20:12,526] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 00:20:12,527] [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_016875225.1	s__VGRW01 sp016875225	77.3565	343	1170	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__VGRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356455.1	s__SMWZ01 sp004356455	76.3437	164	1170	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__SMWZ01	95.0	99.36	99.36	0.81	0.81	2	-
GCA_013215565.1	s__JABSQV01 sp013215565	76.2892	185	1170	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__JABSQV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687015.1	s__GCA-2687015 sp002687015	76.1332	184	1170	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__GCA-2687015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.0819	353	1170	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262315.1	s__PR03 sp018262315	75.7762	161	1170	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	75.7393	157	1170	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003247575.1	s__SZUA-336 sp003247575	75.5998	122	1170	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__SZUA-336	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937385.1	s__QNFN01 sp009937385	75.4886	68	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__QNFN01;f__QNFN01;g__QNFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853315.1	s__REEB422 sp017853315	75.4635	150	1170	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__REEB422	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583835.1	s__Thiococcus pfennigii	75.3694	89	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiococcus	95.0	98.97	98.97	0.88	0.88	2	-
GCA_016214955.1	s__JACRMN01 sp016214955	75.137	151	1170	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JACRMN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825965.1	s__PNKF01 sp902825965	75.0397	92	1170	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426365.1	s__Arenimonas composti	75.0204	120	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.98	99.98	1.00	1.00	2	-
GCA_016192455.1	s__JACPUC01 sp016192455	74.9614	69	1170	d__Bacteria;p__JACPUC01;c__JACPUC01;o__JACPUC01;f__JACPUC01;g__JACPUC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058095.1	s__JABFXX01 sp018058095	74.9614	233	1170	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	99.29	99.24	0.92	0.91	3	-
GCA_018241525.1	s__SZAS-83 sp018241525	74.9526	170	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709145.1	s__JADJEK01 sp016709145	74.8851	123	1170	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JADJEK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793245.1	s__JADKAF01 sp016793245	74.8844	190	1170	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213895.1	s__JACQZJ01 sp016213895	74.8702	128	1170	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JACQZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903912585.1	s__CAIXSE01 sp903912585	74.8418	66	1170	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__UBA2241;f__UBA2241;g__CAIXSE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299835.1	s__Microlunatus_B speluncae	74.8018	109	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795255.1	s__JADJEK01 sp016795255	74.7656	88	1170	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JADJEK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:20:12,529] [INFO] GTDB search result was written to GCA_019310365.1_ASM1931036v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:20:12,529] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:20:12,536] [INFO] DFAST_QC result json was written to GCA_019310365.1_ASM1931036v1_genomic.fna/dqc_result.json
[2023-06-29 00:20:12,536] [INFO] DFAST_QC completed!
[2023-06-29 00:20:12,536] [INFO] Total running time: 0h1m24s