[2024-01-24 15:18:26,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:26,060] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:26,060] [INFO] DQC Reference Directory: /var/lib/cwl/stg3501d9e0-c12e-4ef3-9fa1-101baaa57472/dqc_reference
[2024-01-24 15:18:27,345] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:27,349] [INFO] Task started: Prodigal
[2024-01-24 15:18:27,349] [INFO] Running command: gunzip -c /var/lib/cwl/stge8b74034-a38a-4bfb-8c09-e5c3ee73b985/GCF_003355155.1_ASM335515v1_genomic.fna.gz | prodigal -d GCF_003355155.1_ASM335515v1_genomic.fna/cds.fna -a GCF_003355155.1_ASM335515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:52,837] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:52,837] [INFO] Task started: HMMsearch
[2024-01-24 15:18:52,837] [INFO] Running command: hmmsearch --tblout GCF_003355155.1_ASM335515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3501d9e0-c12e-4ef3-9fa1-101baaa57472/dqc_reference/reference_markers.hmm GCF_003355155.1_ASM335515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:53,248] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:53,250] [INFO] Found 6/6 markers.
[2024-01-24 15:18:53,315] [INFO] Query marker FASTA was written to GCF_003355155.1_ASM335515v1_genomic.fna/markers.fasta
[2024-01-24 15:18:53,316] [INFO] Task started: Blastn
[2024-01-24 15:18:53,316] [INFO] Running command: blastn -query GCF_003355155.1_ASM335515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3501d9e0-c12e-4ef3-9fa1-101baaa57472/dqc_reference/reference_markers.fasta -out GCF_003355155.1_ASM335515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:54,680] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:54,691] [INFO] Selected 27 target genomes.
[2024-01-24 15:18:54,692] [INFO] Target genome list was writen to GCF_003355155.1_ASM335515v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:54,711] [INFO] Task started: fastANI
[2024-01-24 15:18:54,712] [INFO] Running command: fastANI --query /var/lib/cwl/stge8b74034-a38a-4bfb-8c09-e5c3ee73b985/GCF_003355155.1_ASM335515v1_genomic.fna.gz --refList GCF_003355155.1_ASM335515v1_genomic.fna/target_genomes.txt --output GCF_003355155.1_ASM335515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:43,656] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:43,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3501d9e0-c12e-4ef3-9fa1-101baaa57472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:43,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3501d9e0-c12e-4ef3-9fa1-101baaa57472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:43,689] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:43,689] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:43,690] [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 armeniacus	strain=ATCC 15676	GCA_003355155.1	83291	83291	type	True	99.9972	2692	2694	95	conclusive
Streptomyces pathocidini	strain=NRRL B-24287	GCA_001418495.1	1650571	1650571	type	True	81.1471	862	2694	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	81.0953	1201	2694	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	80.876	1142	2694	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	80.8649	1103	2694	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	80.731	1161	2694	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	80.6531	1204	2694	95	below_threshold
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	80.5971	1315	2694	95	below_threshold
Streptomyces lycii	strain=TRM 66187	GCA_009735685.1	2654337	2654337	type	True	80.5235	1212	2694	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	80.3799	988	2694	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	80.1909	1250	2694	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	80.1593	1137	2694	95	below_threshold
Streptomyces xinghaiensis	strain=S187	GCA_000220705.2	1038928	1038928	type	True	80.1532	1176	2694	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.1005	1284	2694	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	79.9375	1112	2694	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	79.9081	1224	2694	95	below_threshold
Streptomyces catenulae	strain=NRRL B-2342	GCA_000718015.1	66875	66875	type	True	79.8773	1120	2694	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	79.8321	956	2694	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	79.7949	1248	2694	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	79.7453	1140	2694	95	below_threshold
Streptomyces mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	79.6684	1181	2694	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	79.6482	1202	2694	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	79.6247	1189	2694	95	below_threshold
Actinacidiphila glaucinigra	strain=CGMCC 4.1858	GCA_900188405.1	235986	235986	type	True	79.3882	1206	2694	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	79.048	1179	2694	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	77.9588	1077	2694	95	below_threshold
Kitasatospora setae	strain=NRRL B-16185	GCA_000716965.1	2066	2066	type	True	77.9206	1051	2694	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:43,692] [INFO] DFAST Taxonomy check result was written to GCF_003355155.1_ASM335515v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:43,693] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:43,693] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:43,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3501d9e0-c12e-4ef3-9fa1-101baaa57472/dqc_reference/checkm_data
[2024-01-24 15:19:43,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:43,777] [INFO] Task started: CheckM
[2024-01-24 15:19:43,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003355155.1_ASM335515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003355155.1_ASM335515v1_genomic.fna/checkm_input GCF_003355155.1_ASM335515v1_genomic.fna/checkm_result
[2024-01-24 15:21:25,263] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:25,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:25,291] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:25,291] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:25,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003355155.1_ASM335515v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:25,292] [INFO] Task started: Blastn
[2024-01-24 15:21:25,292] [INFO] Running command: blastn -query GCF_003355155.1_ASM335515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3501d9e0-c12e-4ef3-9fa1-101baaa57472/dqc_reference/reference_markers_gtdb.fasta -out GCF_003355155.1_ASM335515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:27,342] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:27,346] [INFO] Selected 19 target genomes.
[2024-01-24 15:21:27,346] [INFO] Target genome list was writen to GCF_003355155.1_ASM335515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:27,359] [INFO] Task started: fastANI
[2024-01-24 15:21:27,359] [INFO] Running command: fastANI --query /var/lib/cwl/stge8b74034-a38a-4bfb-8c09-e5c3ee73b985/GCF_003355155.1_ASM335515v1_genomic.fna.gz --refList GCF_003355155.1_ASM335515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003355155.1_ASM335515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:22:00,819] [INFO] Task succeeded: fastANI
[2024-01-24 15:22:00,839] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:22:00,840] [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_003355155.1	s__Streptomyces armeniacus	99.9972	2692	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003665095.1	s__Streptomyces sp003665095	86.744	1678	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424825.1	s__Streptomyces sp000424825	83.1714	1393	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426325.1	s__Streptomyces sp000426325	81.6591	1266	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.50	96.50	0.91	0.91	2	-
GCF_012726235.1	s__Streptomyces sp012726235	81.1626	1253	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001751255.1	s__Streptomyces nanshensis_A	80.9304	1187	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.85	97.85	0.86	0.86	2	-
GCA_000497405.1	s__Streptomyces sp000497405	80.871	1093	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424965.1	s__Streptomyces sp000424965	80.7423	1262	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843305.1	s__Streptomyces barkulensis	80.6967	1132	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	-
GCF_012726265.1	s__Streptomyces sp012726265	80.6853	1292	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426165.1	s__Streptomyces sp000426165	80.5784	1189	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302895.1	s__Streptomyces chlorinus	80.528	1286	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418285.1	s__Streptomyces sp001418285	80.4361	1189	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.71	95.43	0.94	0.89	3	-
GCF_000720725.1	s__Streptomyces rimosus_A	80.1119	1309	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070345.1	s__Streptomyces sp018070345	79.9632	1108	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	79.9349	1218	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_014654785.1	s__Streptomyces mashuensis	79.9183	1116	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018638295.1	s__Streptomyces sp018638295	79.5016	1122	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717185.1	s__Kitasatospora phosalacinea_A	78.0158	1034	2694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:22:00,845] [INFO] GTDB search result was written to GCF_003355155.1_ASM335515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:22:00,845] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:22:00,852] [INFO] DFAST_QC result json was written to GCF_003355155.1_ASM335515v1_genomic.fna/dqc_result.json
[2024-01-24 15:22:00,852] [INFO] DFAST_QC completed!
[2024-01-24 15:22:00,852] [INFO] Total running time: 0h3m35s