[2023-06-29 22:34:39,174] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:34:39,176] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:34:39,176] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd0180ff-1413-4f7a-a748-679618a10270/dqc_reference
[2023-06-29 22:34:40,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:34:40,418] [INFO] Task started: Prodigal
[2023-06-29 22:34:40,419] [INFO] Running command: gunzip -c /var/lib/cwl/stgfde4145a-eac4-4fc4-87c2-91a8ea2c937b/GCA_016183035.1_ASM1618303v1_genomic.fna.gz | prodigal -d GCA_016183035.1_ASM1618303v1_genomic.fna/cds.fna -a GCA_016183035.1_ASM1618303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:35:04,574] [INFO] Task succeeded: Prodigal
[2023-06-29 22:35:04,574] [INFO] Task started: HMMsearch
[2023-06-29 22:35:04,574] [INFO] Running command: hmmsearch --tblout GCA_016183035.1_ASM1618303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd0180ff-1413-4f7a-a748-679618a10270/dqc_reference/reference_markers.hmm GCA_016183035.1_ASM1618303v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:35:05,015] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:35:05,017] [INFO] Found 6/6 markers.
[2023-06-29 22:35:05,083] [INFO] Query marker FASTA was written to GCA_016183035.1_ASM1618303v1_genomic.fna/markers.fasta
[2023-06-29 22:35:05,084] [INFO] Task started: Blastn
[2023-06-29 22:35:05,084] [INFO] Running command: blastn -query GCA_016183035.1_ASM1618303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd0180ff-1413-4f7a-a748-679618a10270/dqc_reference/reference_markers.fasta -out GCA_016183035.1_ASM1618303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:35:05,816] [INFO] Task succeeded: Blastn
[2023-06-29 22:35:05,823] [INFO] Selected 34 target genomes.
[2023-06-29 22:35:05,824] [INFO] Target genome list was writen to GCA_016183035.1_ASM1618303v1_genomic.fna/target_genomes.txt
[2023-06-29 22:35:05,844] [INFO] Task started: fastANI
[2023-06-29 22:35:05,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde4145a-eac4-4fc4-87c2-91a8ea2c937b/GCA_016183035.1_ASM1618303v1_genomic.fna.gz --refList GCA_016183035.1_ASM1618303v1_genomic.fna/target_genomes.txt --output GCA_016183035.1_ASM1618303v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:35:36,997] [INFO] Task succeeded: fastANI
[2023-06-29 22:35:36,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd0180ff-1413-4f7a-a748-679618a10270/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:35:36,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd0180ff-1413-4f7a-a748-679618a10270/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:35:37,021] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:35:37,021] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:35:37,021] [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
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.9388	104	2815	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	74.9383	98	2815	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	74.8991	97	2815	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.8979	115	2815	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.8492	203	2815	95	below_threshold
Lysobacter bugurensis	strain=KCTC 23077	GCA_014652095.1	543356	543356	type	True	74.8484	79	2815	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	74.8398	71	2815	95	below_threshold
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	74.8016	63	2815	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.7798	109	2815	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	74.7774	126	2815	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	74.7734	130	2815	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.7695	324	2815	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.7609	307	2815	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	74.7557	120	2815	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	74.7403	64	2815	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	74.7297	95	2815	95	below_threshold
Amycolatopsis thermoflava	strain=N1165	GCA_000473265.1	84480	84480	type	True	74.724	133	2815	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	74.7067	55	2815	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	74.678	103	2815	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	74.6772	107	2815	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	74.6746	57	2815	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	74.6712	98	2815	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	74.6688	99	2815	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	74.6685	132	2815	95	below_threshold
Microbacterium indicum	strain=DSM 19969	GCA_000422385.1	358100	358100	type	True	74.6591	115	2815	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	74.6584	122	2815	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	74.6394	107	2815	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:35:37,023] [INFO] DFAST Taxonomy check result was written to GCA_016183035.1_ASM1618303v1_genomic.fna/tc_result.tsv
[2023-06-29 22:35:37,024] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:35:37,024] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:35:37,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd0180ff-1413-4f7a-a748-679618a10270/dqc_reference/checkm_data
[2023-06-29 22:35:37,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:35:37,107] [INFO] Task started: CheckM
[2023-06-29 22:35:37,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016183035.1_ASM1618303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016183035.1_ASM1618303v1_genomic.fna/checkm_input GCA_016183035.1_ASM1618303v1_genomic.fna/checkm_result
[2023-06-29 22:36:55,700] [INFO] Task succeeded: CheckM
[2023-06-29 22:36:55,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:36:55,732] [INFO] ===== Completeness check finished =====
[2023-06-29 22:36:55,732] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:36:55,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016183035.1_ASM1618303v1_genomic.fna/markers.fasta)
[2023-06-29 22:36:55,733] [INFO] Task started: Blastn
[2023-06-29 22:36:55,733] [INFO] Running command: blastn -query GCA_016183035.1_ASM1618303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd0180ff-1413-4f7a-a748-679618a10270/dqc_reference/reference_markers_gtdb.fasta -out GCA_016183035.1_ASM1618303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:36:56,671] [INFO] Task succeeded: Blastn
[2023-06-29 22:36:56,677] [INFO] Selected 44 target genomes.
[2023-06-29 22:36:56,677] [INFO] Target genome list was writen to GCA_016183035.1_ASM1618303v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:36:56,697] [INFO] Task started: fastANI
[2023-06-29 22:36:56,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde4145a-eac4-4fc4-87c2-91a8ea2c937b/GCA_016183035.1_ASM1618303v1_genomic.fna.gz --refList GCA_016183035.1_ASM1618303v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016183035.1_ASM1618303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:37:33,808] [INFO] Task succeeded: fastANI
[2023-06-29 22:37:33,835] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 22:37:33,836] [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_011526105.1	s__WYAZ01 sp011526105	75.7104	208	2815	d__Bacteria;p__Myxococcota;c__WYAZ01;o__WYAZ01;f__WYAZ01;g__WYAZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002408385.1	s__UBA10939 sp002408385	74.9886	175	2815	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__UBA5297;g__UBA10939	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692505.1	s__SHZC01 sp009692505	74.9744	91	2815	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA7976;f__UBA1532;g__SHZC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016177705.1	s__JACOUT01 sp016177705	74.9483	214	2815	d__Bacteria;p__Myxococcota;c__UBA727;o__UBA727;f__VGSZ01;g__JACOUT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266075.1	s__SZAS-1 sp018266075	74.9346	172	2815	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__SZAS-1;g__SZAS-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016184115.1	s__JACPDH01 sp016184115	74.9072	82	2815	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JACPDH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	74.8991	304	2815	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218825.1	s__JACRCV01 sp016218825	74.8911	191	2815	d__Bacteria;p__Myxococcota;c__XYA12-FULL-58-9;o__XYA12-FULL-58-9;f__XYA12-FULL-58-9;g__JACRCV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649845.1	s__Polyangium spumosum	74.8909	327	2815	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794345.1	s__CAITIQ01 sp016794345	74.8893	256	2815	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITIQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901538445.1	s__Gemmata sp901538445	74.8875	133	2815	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526095.1	s__WYBA01 sp011526095	74.8764	358	2815	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794525.1	s__UBA2376 sp016794525	74.826	304	2815	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696455.1	s__UBA2376 sp900696455	74.8178	250	2815	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCA_003577305.1	s__SCN-69-89 sp003577305	74.8163	70	2815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.77	99.54	0.93	0.87	4	-
GCF_000418325.1	s__Sorangium cellulosum_D	74.8155	376	2815	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCA_017853315.1	s__REEB422 sp017853315	74.7919	121	2815	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__REEB422	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707895.1	s__UBA2376 sp016707895	74.7911	281	2815	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
GCA_005879245.1	s__DP-23 sp005879245	74.7895	58	2815	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-23	95.0	97.46	97.46	0.74	0.74	2	-
GCA_016794545.1	s__JABFXX01 sp016794545	74.7865	295	2815	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699025.1	s__GCA-2699025 sp002699025	74.7621	334	2815	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__GCA-2699025	95.0	99.90	99.85	0.97	0.97	3	-
GCA_018780435.1	s__SXOO01 sp018780435	74.762	177	2815	d__Bacteria;p__Myxococcota;c__UBA9042;o__GCA-2863065;f__GCA-2863065;g__SXOO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970825.1	s__REEB422 sp018970825	74.7027	95	2815	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__REEB422	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241525.1	s__SZAS-83 sp018241525	74.7018	121	2815	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_003222535.1	s__Gp6-AA45 sp003222535	74.6921	121	2815	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.30	99.28	0.90	0.90	3	-
GCA_016930215.1	s__JAAZOP01 sp016930215	74.6783	134	2815	d__Bacteria;p__Myxococcota;c__Polyangia;o__DRWM01;f__JAAZOP01;g__JAAZOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004143945.1	s__Dokdonella_A sp004143945	74.6751	115	2815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704895.1	s__VBCG01 sp016704895	74.6743	132	2815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	96.62	96.45	0.90	0.90	3	-
GCA_002297645.1	s__Dokdonella_A sp002297645	74.674	70	2815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCF_001421485.1	s__Agreia sp001421485	74.6572	69	2815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agreia	95.0	97.75	97.58	0.92	0.91	3	-
GCA_016861105.1	s__VBCG01 sp016861105	74.6479	127	2815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177765.1	s__Agreia sp900177765	74.6356	56	2815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agreia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884235.1	s__CAIYLH01 sp903884235	74.6335	92	2815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.42	99.08	0.95	0.88	22	-
--------------------------------------------------------------------------------
[2023-06-29 22:37:33,838] [INFO] GTDB search result was written to GCA_016183035.1_ASM1618303v1_genomic.fna/result_gtdb.tsv
[2023-06-29 22:37:33,839] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:37:33,845] [INFO] DFAST_QC result json was written to GCA_016183035.1_ASM1618303v1_genomic.fna/dqc_result.json
[2023-06-29 22:37:33,845] [INFO] DFAST_QC completed!
[2023-06-29 22:37:33,845] [INFO] Total running time: 0h2m55s