[2024-01-24 13:37:19,449] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:19,451] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:19,451] [INFO] DQC Reference Directory: /var/lib/cwl/stg298ea979-8109-4c3d-978b-a5d877056fe8/dqc_reference
[2024-01-24 13:37:20,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:20,947] [INFO] Task started: Prodigal
[2024-01-24 13:37:20,948] [INFO] Running command: gunzip -c /var/lib/cwl/stg943fbde3-89a2-4447-b06b-a8745391036b/GCF_012273655.1_ASM1227365v1_genomic.fna.gz | prodigal -d GCF_012273655.1_ASM1227365v1_genomic.fna/cds.fna -a GCF_012273655.1_ASM1227365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:44,327] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:44,327] [INFO] Task started: HMMsearch
[2024-01-24 13:37:44,327] [INFO] Running command: hmmsearch --tblout GCF_012273655.1_ASM1227365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg298ea979-8109-4c3d-978b-a5d877056fe8/dqc_reference/reference_markers.hmm GCF_012273655.1_ASM1227365v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:44,699] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:44,700] [INFO] Found 6/6 markers.
[2024-01-24 13:37:44,765] [INFO] Query marker FASTA was written to GCF_012273655.1_ASM1227365v1_genomic.fna/markers.fasta
[2024-01-24 13:37:44,766] [INFO] Task started: Blastn
[2024-01-24 13:37:44,766] [INFO] Running command: blastn -query GCF_012273655.1_ASM1227365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg298ea979-8109-4c3d-978b-a5d877056fe8/dqc_reference/reference_markers.fasta -out GCF_012273655.1_ASM1227365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:46,207] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:46,211] [INFO] Selected 29 target genomes.
[2024-01-24 13:37:46,211] [INFO] Target genome list was writen to GCF_012273655.1_ASM1227365v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:46,268] [INFO] Task started: fastANI
[2024-01-24 13:37:46,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg943fbde3-89a2-4447-b06b-a8745391036b/GCF_012273655.1_ASM1227365v1_genomic.fna.gz --refList GCF_012273655.1_ASM1227365v1_genomic.fna/target_genomes.txt --output GCF_012273655.1_ASM1227365v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:44,213] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:44,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg298ea979-8109-4c3d-978b-a5d877056fe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:44,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg298ea979-8109-4c3d-978b-a5d877056fe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:44,246] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:44,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:44,247] [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 physcomitrii	strain=LD120	GCA_012273655.1	2724184	2724184	type	True	100.0	2517	2520	95	conclusive
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	82.0544	1319	2520	95	below_threshold
Streptomyces bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	81.9448	1286	2520	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_004784465.1	29306	29306	type	True	81.9255	1246	2520	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	81.9033	1391	2520	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	81.8109	1367	2520	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	81.7545	1415	2520	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.7237	1206	2520	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	81.6383	1355	2520	95	below_threshold
Streptomyces zinciresistens	strain=K42	GCA_000225525.2	1073330	1073330	type	True	81.6033	1266	2520	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	81.523	1396	2520	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.5204	1363	2520	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.4439	1343	2520	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	81.3661	1222	2520	95	below_threshold
Streptomyces apocyni	strain=TRM 66233	GCA_009739465.1	2654677	2654677	type	True	81.3529	1173	2520	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	81.2858	1335	2520	95	below_threshold
Streptomyces roseicoloratus	strain=TRM44457	GCA_004117935.1	2508722	2508722	type	True	81.266	1236	2520	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	81.2556	1341	2520	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	81.2341	1323	2520	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	81.135	1275	2520	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	81.0757	1011	2520	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	81.0698	1301	2520	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_003568675.1	2315329	2315329	type	True	81.0321	1308	2520	95	below_threshold
Streptomyces abyssomicinicus	strain=CHI39	GCA_008974245.1	574929	574929	type	True	80.9324	1246	2520	95	below_threshold
Streptomyces lycii	strain=TRM 66187	GCA_009735685.1	2654337	2654337	type	True	80.646	1127	2520	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	80.254	1197	2520	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	80.184	1007	2520	95	below_threshold
Kitasatospora setae	strain=NRRL B-16185	GCA_000716965.1	2066	2066	type	True	78.7856	1104	2520	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	78.7592	1138	2520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:44,248] [INFO] DFAST Taxonomy check result was written to GCF_012273655.1_ASM1227365v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:44,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:44,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:44,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg298ea979-8109-4c3d-978b-a5d877056fe8/dqc_reference/checkm_data
[2024-01-24 13:38:44,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:44,323] [INFO] Task started: CheckM
[2024-01-24 13:38:44,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012273655.1_ASM1227365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012273655.1_ASM1227365v1_genomic.fna/checkm_input GCF_012273655.1_ASM1227365v1_genomic.fna/checkm_result
[2024-01-24 13:40:31,251] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:31,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:31,274] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:31,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:31,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012273655.1_ASM1227365v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:31,275] [INFO] Task started: Blastn
[2024-01-24 13:40:31,275] [INFO] Running command: blastn -query GCF_012273655.1_ASM1227365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg298ea979-8109-4c3d-978b-a5d877056fe8/dqc_reference/reference_markers_gtdb.fasta -out GCF_012273655.1_ASM1227365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:33,625] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:33,628] [INFO] Selected 23 target genomes.
[2024-01-24 13:40:33,628] [INFO] Target genome list was writen to GCF_012273655.1_ASM1227365v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:33,647] [INFO] Task started: fastANI
[2024-01-24 13:40:33,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg943fbde3-89a2-4447-b06b-a8745391036b/GCF_012273655.1_ASM1227365v1_genomic.fna.gz --refList GCF_012273655.1_ASM1227365v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012273655.1_ASM1227365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:19,369] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:19,387] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:19,388] [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_012273655.1	s__Streptomyces physcomitrii	100.0	2517	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.15	97.14	0.94	0.93	4	conclusive
GCF_013364195.1	s__Streptomyces sp013364195	84.7587	1626	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002154585.1	s__Streptomyces pseudogriseolus	81.9519	1153	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.58	96.58	0.90	0.87	9	-
GCF_001654495.1	s__Streptomyces sp001654495	81.9305	1391	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.91	96.91	0.92	0.92	2	-
GCA_014650475.1	s__Streptomyces albogriseolus	81.8837	1327	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.59	97.23	0.93	0.90	7	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	81.8711	1397	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_014648855.1	s__Streptomyces parvulus	81.8627	1394	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.93	0.93	0.87	4	-
GCF_003664315.1	s__Streptomyces sp003664315	81.8133	1397	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649355.1	s__Streptomyces althioticus	81.6539	1336	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.43	96.72	0.91	0.83	9	-
GCF_014596915.1	s__Streptomyces sp014596915	81.6235	1377	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342105.1	s__Streptomyces sp004342105	81.4319	1331	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604455.1	s__Streptomyces sp009604455	81.4115	1360	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610995.1	s__Streptomyces sp003116725	81.3719	1295	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.40	95.27	0.92	0.85	7	-
GCF_003384795.1	s__Streptomyces sp003384795	81.3048	1384	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105755.1	s__Streptomyces sp900105755	81.2957	1402	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	81.286	1316	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCF_014647875.1	s__Streptomyces brasiliensis	81.2729	1337	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117935.1	s__Streptomyces roseicoloratus	81.2305	1243	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718135.1	s__Streptomyces cyaneofuscatus	81.1498	1322	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	95.81	0.91	0.85	12	-
GCF_001905345.1	s__Streptomyces uncialis	80.9743	1308	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.41	97.41	0.92	0.92	4	-
GCF_012726235.1	s__Streptomyces sp012726235	80.2886	1109	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000514715.1	s__Streptomyces sp000514715	79.5187	1156	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847285.1	s__Streptomyces sp002847285	79.4538	1196	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.16	95.03	0.85	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:19,390] [INFO] GTDB search result was written to GCF_012273655.1_ASM1227365v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:19,391] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:19,396] [INFO] DFAST_QC result json was written to GCF_012273655.1_ASM1227365v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:19,397] [INFO] DFAST_QC completed!
[2024-01-24 13:41:19,397] [INFO] Total running time: 0h3m60s