[2024-01-24 13:49:54,855] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:54,856] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:54,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg91116a0f-037f-43d9-8b6f-e3a835292b3f/dqc_reference
[2024-01-24 13:49:55,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:55,958] [INFO] Task started: Prodigal
[2024-01-24 13:49:55,958] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbf88e30-ab0f-4a69-81a3-d3f9751c02be/GCF_019890615.1_ASM1989061v1_genomic.fna.gz | prodigal -d GCF_019890615.1_ASM1989061v1_genomic.fna/cds.fna -a GCF_019890615.1_ASM1989061v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:15,215] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:15,215] [INFO] Task started: HMMsearch
[2024-01-24 13:50:15,215] [INFO] Running command: hmmsearch --tblout GCF_019890615.1_ASM1989061v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91116a0f-037f-43d9-8b6f-e3a835292b3f/dqc_reference/reference_markers.hmm GCF_019890615.1_ASM1989061v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:15,495] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:15,496] [INFO] Found 6/6 markers.
[2024-01-24 13:50:15,548] [INFO] Query marker FASTA was written to GCF_019890615.1_ASM1989061v1_genomic.fna/markers.fasta
[2024-01-24 13:50:15,548] [INFO] Task started: Blastn
[2024-01-24 13:50:15,548] [INFO] Running command: blastn -query GCF_019890615.1_ASM1989061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91116a0f-037f-43d9-8b6f-e3a835292b3f/dqc_reference/reference_markers.fasta -out GCF_019890615.1_ASM1989061v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:16,848] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:16,851] [INFO] Selected 28 target genomes.
[2024-01-24 13:50:16,851] [INFO] Target genome list was writen to GCF_019890615.1_ASM1989061v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:16,858] [INFO] Task started: fastANI
[2024-01-24 13:50:16,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbf88e30-ab0f-4a69-81a3-d3f9751c02be/GCF_019890615.1_ASM1989061v1_genomic.fna.gz --refList GCF_019890615.1_ASM1989061v1_genomic.fna/target_genomes.txt --output GCF_019890615.1_ASM1989061v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:04,490] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:04,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91116a0f-037f-43d9-8b6f-e3a835292b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:04,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91116a0f-037f-43d9-8b6f-e3a835292b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:04,506] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:51:04,506] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:04,506] [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
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	100.0	2434	2435	95	conclusive
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	83.3441	1212	2435	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	81.0792	963	2435	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	81.0504	1093	2435	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	80.9729	1182	2435	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	80.8955	1078	2435	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	80.8797	1030	2435	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	80.865	1134	2435	95	below_threshold
Streptomyces caatingaensis	strain=CMAA 1322	GCA_001187435.1	1678637	1678637	type	True	80.8238	1075	2435	95	below_threshold
Streptomyces niger	strain=NRRL B-3857	GCA_000718305.1	66373	66373	type	True	80.8194	1094	2435	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	80.7783	1151	2435	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	80.7782	1002	2435	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.7521	1135	2435	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	80.6976	1011	2435	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	80.6346	1130	2435	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	80.5286	1198	2435	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	80.5025	1108	2435	95	below_threshold
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	80.4856	1020	2435	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	80.4827	1170	2435	95	below_threshold
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	80.4771	1134	2435	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	80.3824	1126	2435	95	below_threshold
Streptomyces spongiicola	strain=HNM0071	GCA_003122365.1	1690221	1690221	type	True	80.2771	982	2435	95	below_threshold
Streptomyces marianii	strain=ICN19	GCA_005795905.1	1817406	1817406	type	True	80.2626	1034	2435	95	below_threshold
Streptomyces xantholiticus	strain=JCM 4863	GCA_014651015.1	68285	68285	type	True	80.197	968	2435	95	below_threshold
Kitasatospora indigofera	strain=JCM 4646	GCA_014655955.1	67307	67307	type	True	79.2138	1103	2435	95	below_threshold
Kitasatospora herbaricolor	strain=JCM 4138	GCA_014648975.1	68217	68217	type	True	79.1472	1098	2435	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	77.1352	727	2435	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	76.6008	800	2435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:04,507] [INFO] DFAST Taxonomy check result was written to GCF_019890615.1_ASM1989061v1_genomic.fna/tc_result.tsv
[2024-01-24 13:51:04,508] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:04,508] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:04,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91116a0f-037f-43d9-8b6f-e3a835292b3f/dqc_reference/checkm_data
[2024-01-24 13:51:04,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:04,575] [INFO] Task started: CheckM
[2024-01-24 13:51:04,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019890615.1_ASM1989061v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019890615.1_ASM1989061v1_genomic.fna/checkm_input GCF_019890615.1_ASM1989061v1_genomic.fna/checkm_result
[2024-01-24 13:52:35,093] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:35,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.54%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:35,110] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:35,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:35,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019890615.1_ASM1989061v1_genomic.fna/markers.fasta)
[2024-01-24 13:52:35,111] [INFO] Task started: Blastn
[2024-01-24 13:52:35,111] [INFO] Running command: blastn -query GCF_019890615.1_ASM1989061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91116a0f-037f-43d9-8b6f-e3a835292b3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019890615.1_ASM1989061v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:37,267] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:37,270] [INFO] Selected 32 target genomes.
[2024-01-24 13:52:37,270] [INFO] Target genome list was writen to GCF_019890615.1_ASM1989061v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:37,307] [INFO] Task started: fastANI
[2024-01-24 13:52:37,307] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbf88e30-ab0f-4a69-81a3-d3f9751c02be/GCF_019890615.1_ASM1989061v1_genomic.fna.gz --refList GCF_019890615.1_ASM1989061v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019890615.1_ASM1989061v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:30,030] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:30,047] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:53:30,048] [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
GCF_003144095.1	s__Streptomyces sp003144095	93.8872	1846	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000240165.1	s__Streptomyces cattleya	82.9204	1334	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001418495.1	s__Streptomyces pathocidini	81.782	790	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083985.1	s__SCUT-3 sp014083985	81.1452	997	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__SCUT-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016916835.1	s__Streptomyces bryophytorum	81.0332	1095	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_900110255.1	s__Streptomyces rubidus	81.0	1176	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	80.9352	1126	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654785.1	s__Streptomyces mashuensis	80.8977	1078	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383935.1	s__Streptomyces sp000383935	80.8787	1204	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_000718305.1	s__Streptomyces niger	80.8441	1090	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010548465.1	s__Streptomyces sp010548465	80.8395	881	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187435.1	s__Streptomyces caatingaensis	80.8348	1074	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999245.1	s__Streptomyces sp015999245	80.781	1062	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916255.1	s__Streptomyces mobaraensis	80.76	1090	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
GCF_000761215.1	s__Streptomyces glaucescens	80.6764	1104	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270575.1	s__Streptomyces decoyicus	80.6114	1095	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_001553455.1	s__Streptomyces hygroscopicus	80.5664	1051	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
GCF_009811555.1	s__Streptomyces caniferus	80.5502	1192	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719555.1	s__Streptomyces sp000719555	80.5072	1073	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927245.1	s__Streptomyces sp012927245	80.4834	1022	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014649795.1	s__Streptomyces melanogenes	80.4531	1175	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_008042045.1	s__Streptomyces sp008042045	80.441	1082	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646055.1	s__Streptomyces_A tyrosinilyticus	80.4333	1016	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069625.1	s__Streptomyces yatensis	80.4326	1141	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	N/A	N/A	N/A	N/A	1	-
GCF_008271805.1	s__Streptomyces sp008271805	80.3431	976	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122365.1	s__Streptomyces spongiicola	80.2756	983	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.39	99.39	0.96	0.96	2	-
GCF_000147815.2	s__Streptomyces violaceusniger_A	80.2226	1127	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3301	95.69	95.54	0.80	0.80	4	-
GCF_015689475.1	s__Streptomyces solisilvae	79.9947	1163	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	97.94	0.94	0.86	10	-
GCF_014648975.1	s__Kitasatospora herbaricolor	79.1337	1101	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.20	96.20	0.86	0.86	2	-
GCF_900108175.1	s__Thermomonospora echinospora	77.1533	720	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760925.1	s__Nonomuraea typhae	76.5964	800	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019245115.1	s__JAFARZ01 sp019245115	75.9452	463	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__JAFARZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:30,050] [INFO] GTDB search result was written to GCF_019890615.1_ASM1989061v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:30,051] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:30,055] [INFO] DFAST_QC result json was written to GCF_019890615.1_ASM1989061v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:30,056] [INFO] DFAST_QC completed!
[2024-01-24 13:53:30,056] [INFO] Total running time: 0h3m35s