[2023-06-17 07:12:15,046] [INFO] DFAST_QC pipeline started.
[2023-06-17 07:12:15,068] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 07:12:15,068] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf7f2d5d-560c-4671-a098-e300d5cb070b/dqc_reference
[2023-06-17 07:12:16,822] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 07:12:16,823] [INFO] Task started: Prodigal
[2023-06-17 07:12:16,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg8825747b-c4cd-4f5f-be18-71c3c5cf230b/GCA_009692585.1_ASM969258v1_genomic.fna.gz | prodigal -d GCA_009692585.1_ASM969258v1_genomic.fna/cds.fna -a GCA_009692585.1_ASM969258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:12:30,920] [INFO] Task succeeded: Prodigal
[2023-06-17 07:12:30,921] [INFO] Task started: HMMsearch
[2023-06-17 07:12:30,921] [INFO] Running command: hmmsearch --tblout GCA_009692585.1_ASM969258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf7f2d5d-560c-4671-a098-e300d5cb070b/dqc_reference/reference_markers.hmm GCA_009692585.1_ASM969258v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:12:31,217] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:12:31,218] [INFO] Found 6/6 markers.
[2023-06-17 07:12:31,267] [INFO] Query marker FASTA was written to GCA_009692585.1_ASM969258v1_genomic.fna/markers.fasta
[2023-06-17 07:12:31,267] [INFO] Task started: Blastn
[2023-06-17 07:12:31,268] [INFO] Running command: blastn -query GCA_009692585.1_ASM969258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf7f2d5d-560c-4671-a098-e300d5cb070b/dqc_reference/reference_markers.fasta -out GCA_009692585.1_ASM969258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:12:31,979] [INFO] Task succeeded: Blastn
[2023-06-17 07:12:31,983] [INFO] Selected 36 target genomes.
[2023-06-17 07:12:31,983] [INFO] Target genome list was writen to GCA_009692585.1_ASM969258v1_genomic.fna/target_genomes.txt
[2023-06-17 07:12:32,016] [INFO] Task started: fastANI
[2023-06-17 07:12:32,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg8825747b-c4cd-4f5f-be18-71c3c5cf230b/GCA_009692585.1_ASM969258v1_genomic.fna.gz --refList GCA_009692585.1_ASM969258v1_genomic.fna/target_genomes.txt --output GCA_009692585.1_ASM969258v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 07:13:04,796] [INFO] Task succeeded: fastANI
[2023-06-17 07:13:04,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf7f2d5d-560c-4671-a098-e300d5cb070b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 07:13:04,797] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf7f2d5d-560c-4671-a098-e300d5cb070b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 07:13:04,823] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 07:13:04,823] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 07:13:04,823] [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
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	75.0586	51	1554	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	74.7984	69	1554	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.7969	104	1554	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	74.7918	83	1554	95	below_threshold
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	74.7891	114	1554	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	74.7854	119	1554	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	74.7747	144	1554	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	74.7704	144	1554	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	74.7247	90	1554	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	74.7242	119	1554	95	below_threshold
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	74.7236	96	1554	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	74.7217	92	1554	95	below_threshold
Streptomyces specialis	strain=type strain: GW41-1564	GCA_001493375.1	498367	498367	type	True	74.7211	108	1554	95	below_threshold
Demequina iriomotensis	strain=NBRC 109399	GCA_000971395.1	1536641	1536641	type	True	74.7205	71	1554	95	below_threshold
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	74.716	64	1554	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.712	99	1554	95	below_threshold
Comamonas serinivorans	strain=DSM 26136	GCA_002158865.1	1082851	1082851	type	True	74.704	52	1554	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	74.6938	66	1554	95	below_threshold
Burkholderia cenocepacia	strain=NCTC13227	GCA_900446215.1	95486	95486	type	True	74.6816	118	1554	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	74.6661	71	1554	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	74.6648	166	1554	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	74.6424	69	1554	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	74.6386	95	1554	95	below_threshold
Streptomyces xiaopingdaonensis	strain=DUT 180	GCA_000262345.1	1565415	1565415	type	True	74.6267	112	1554	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	74.6255	86	1554	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	74.6166	51	1554	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	74.615	176	1554	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	74.5897	63	1554	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	74.5865	66	1554	95	below_threshold
Streptomyces sulphureus	strain=DSM 40104	GCA_000381025.1	47758	47758	type	True	74.5803	113	1554	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 07:13:04,826] [INFO] DFAST Taxonomy check result was written to GCA_009692585.1_ASM969258v1_genomic.fna/tc_result.tsv
[2023-06-17 07:13:04,827] [INFO] ===== Taxonomy check completed =====
[2023-06-17 07:13:04,827] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:13:04,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf7f2d5d-560c-4671-a098-e300d5cb070b/dqc_reference/checkm_data
[2023-06-17 07:13:04,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:13:04,886] [INFO] Task started: CheckM
[2023-06-17 07:13:04,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009692585.1_ASM969258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009692585.1_ASM969258v1_genomic.fna/checkm_input GCA_009692585.1_ASM969258v1_genomic.fna/checkm_result
[2023-06-17 07:13:48,376] [INFO] Task succeeded: CheckM
[2023-06-17 07:13:48,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 12.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 07:13:48,403] [INFO] ===== Completeness check finished =====
[2023-06-17 07:13:48,403] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:13:48,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009692585.1_ASM969258v1_genomic.fna/markers.fasta)
[2023-06-17 07:13:48,404] [INFO] Task started: Blastn
[2023-06-17 07:13:48,404] [INFO] Running command: blastn -query GCA_009692585.1_ASM969258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf7f2d5d-560c-4671-a098-e300d5cb070b/dqc_reference/reference_markers_gtdb.fasta -out GCA_009692585.1_ASM969258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:13:49,294] [INFO] Task succeeded: Blastn
[2023-06-17 07:13:49,300] [INFO] Selected 16 target genomes.
[2023-06-17 07:13:49,300] [INFO] Target genome list was writen to GCA_009692585.1_ASM969258v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:13:49,317] [INFO] Task started: fastANI
[2023-06-17 07:13:49,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg8825747b-c4cd-4f5f-be18-71c3c5cf230b/GCA_009692585.1_ASM969258v1_genomic.fna.gz --refList GCA_009692585.1_ASM969258v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009692585.1_ASM969258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:14:03,784] [INFO] Task succeeded: fastANI
[2023-06-17 07:14:03,801] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:14:03,802] [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_009692585.1	s__SXON01 sp009692585	100.0	1545	1554	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005776735.1	s__SXON01 sp005776735	78.0958	568	1554	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885375.1	s__SXON01 sp903885375	77.7193	590	1554	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.89	0.96	0.95	10	-
GCA_903921785.1	s__SXON01 sp903921785	77.682	598	1554	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.91	0.96	0.95	4	-
GCA_016875435.1	s__SXON01 sp016875435	77.2622	406	1554	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875315.1	s__SXON01 sp016875315	77.2264	411	1554	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014191855.1	s__SXON01 sp014191855	76.9885	486	1554	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778355.1	s__SXON01 sp005778355	76.7421	403	1554	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.89	99.88	0.95	0.94	3	-
GCA_903959175.1	s__CAJBVW01 sp903959175	76.4388	355	1554	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAJBVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692605.1	s__CAIUMM01 sp009692605	76.0476	133	1554	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAIUMM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861005.1	s__CAIOSP01 sp903861005	75.387	155	1554	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__CAIOSP01	95.0	99.96	99.95	0.97	0.97	4	-
GCF_003024235.1	s__Arenimonas caeni	74.7819	87	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005792545.1	s__SXRM01 sp005792545	74.7568	83	1554	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__SXRM01	95.0	99.92	99.92	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-17 07:14:03,804] [INFO] GTDB search result was written to GCA_009692585.1_ASM969258v1_genomic.fna/result_gtdb.tsv
[2023-06-17 07:14:03,804] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:14:03,809] [INFO] DFAST_QC result json was written to GCA_009692585.1_ASM969258v1_genomic.fna/dqc_result.json
[2023-06-17 07:14:03,810] [INFO] DFAST_QC completed!
[2023-06-17 07:14:03,810] [INFO] Total running time: 0h1m49s