[2024-01-24 14:39:15,011] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,013] [INFO] DQC Reference Directory: /var/lib/cwl/stga31307ca-68e4-42e9-aa56-2b07689ef739/dqc_reference
[2024-01-24 14:39:16,350] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,351] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,351] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3d432f7-e9b0-4b69-9077-8dc443aadc15/GCF_005981925.1_ASM598192v1_genomic.fna.gz | prodigal -d GCF_005981925.1_ASM598192v1_genomic.fna/cds.fna -a GCF_005981925.1_ASM598192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:35,019] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:35,020] [INFO] Task started: HMMsearch
[2024-01-24 14:39:35,020] [INFO] Running command: hmmsearch --tblout GCF_005981925.1_ASM598192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga31307ca-68e4-42e9-aa56-2b07689ef739/dqc_reference/reference_markers.hmm GCF_005981925.1_ASM598192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:35,372] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:35,373] [INFO] Found 6/6 markers.
[2024-01-24 14:39:35,432] [INFO] Query marker FASTA was written to GCF_005981925.1_ASM598192v1_genomic.fna/markers.fasta
[2024-01-24 14:39:35,433] [INFO] Task started: Blastn
[2024-01-24 14:39:35,433] [INFO] Running command: blastn -query GCF_005981925.1_ASM598192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga31307ca-68e4-42e9-aa56-2b07689ef739/dqc_reference/reference_markers.fasta -out GCF_005981925.1_ASM598192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:36,807] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:36,811] [INFO] Selected 20 target genomes.
[2024-01-24 14:39:36,812] [INFO] Target genome list was writen to GCF_005981925.1_ASM598192v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:36,823] [INFO] Task started: fastANI
[2024-01-24 14:39:36,823] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3d432f7-e9b0-4b69-9077-8dc443aadc15/GCF_005981925.1_ASM598192v1_genomic.fna.gz --refList GCF_005981925.1_ASM598192v1_genomic.fna/target_genomes.txt --output GCF_005981925.1_ASM598192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:09,191] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:09,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga31307ca-68e4-42e9-aa56-2b07689ef739/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:09,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga31307ca-68e4-42e9-aa56-2b07689ef739/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:09,206] [INFO] Found 20 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:40:09,207] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:40:09,207] [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 albidochromogenes	strain=DSM 41800	GCA_005981925.1	329524	329524	type	True	100.0	2027	2056	95	inconclusive
Streptomyces chryseus	strain=JCM 4737	GCA_014650755.1	68186	68186	type	True	95.5357	1656	2056	95	inconclusive
Streptomyces chryseus	strain=DSM 40420	GCA_005981935.1	68186	68186	type	True	95.3135	1347	2056	95	inconclusive
Streptomyces flavidovirens	strain=DSM 40150	GCA_000429085.1	67298	67298	type	True	90.3254	1508	2056	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.4465	1231	2056	95	below_threshold
Streptomyces gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	83.3302	1157	2056	95	below_threshold
Streptomyces finlayi	strain=JCM 4637	GCA_014650515.1	67296	67296	type	True	83.3055	1274	2056	95	below_threshold
Streptomyces candidus	strain=JCM 4629	GCA_014655855.1	67283	67283	type	True	83.2916	1212	2056	95	below_threshold
Streptomyces candidus	strain=DSM 40141	GCA_014207445.1	67283	67283	type	True	83.2773	1206	2056	95	below_threshold
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	82.7543	1200	2056	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	82.6629	1161	2056	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.4884	1254	2056	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.182	1148	2056	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	81.8364	1081	2056	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	81.7417	1191	2056	95	below_threshold
Streptomyces fuscigenes	strain=JBL-20	GCA_021556455.1	1528880	1528880	type	True	81.6617	836	2056	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	81.4796	1028	2056	95	below_threshold
Acrocarpospora phusangensis	strain=NBRC 108782	GCA_016862995.1	1070424	1070424	type	True	76.5851	522	2056	95	below_threshold
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	76.5609	249	2056	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	76.3053	279	2056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:09,208] [INFO] DFAST Taxonomy check result was written to GCF_005981925.1_ASM598192v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:09,209] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:09,209] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:09,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga31307ca-68e4-42e9-aa56-2b07689ef739/dqc_reference/checkm_data
[2024-01-24 14:40:09,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:09,275] [INFO] Task started: CheckM
[2024-01-24 14:40:09,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005981925.1_ASM598192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005981925.1_ASM598192v1_genomic.fna/checkm_input GCF_005981925.1_ASM598192v1_genomic.fna/checkm_result
[2024-01-24 14:41:02,494] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:02,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:02,525] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:02,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:02,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005981925.1_ASM598192v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:02,526] [INFO] Task started: Blastn
[2024-01-24 14:41:02,527] [INFO] Running command: blastn -query GCF_005981925.1_ASM598192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga31307ca-68e4-42e9-aa56-2b07689ef739/dqc_reference/reference_markers_gtdb.fasta -out GCF_005981925.1_ASM598192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:04,542] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:04,545] [INFO] Selected 12 target genomes.
[2024-01-24 14:41:04,545] [INFO] Target genome list was writen to GCF_005981925.1_ASM598192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:04,554] [INFO] Task started: fastANI
[2024-01-24 14:41:04,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3d432f7-e9b0-4b69-9077-8dc443aadc15/GCF_005981925.1_ASM598192v1_genomic.fna.gz --refList GCF_005981925.1_ASM598192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005981925.1_ASM598192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:25,632] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:25,642] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:41:25,643] [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_005981925.1	s__Streptomyces albidochromogenes	100.0	2027	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	N/A	N/A	N/A	N/A	1	inconclusive
GCF_014650755.1	s__Streptomyces chryseus	95.523	1657	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	99.26	99.24	0.89	0.85	3	inconclusive
GCF_001746415.1	s__Streptomyces agglomeratus	90.3527	1691	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.39	0.92	0.91	5	-
GCF_000429085.1	s__Streptomyces flavidovirens	90.3252	1508	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.82	0.82	2	-
GCF_018614035.1	s__Streptomyces sp018614035	89.6284	1495	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614615.1	s__Streptomyces sp018614615	89.5333	1522	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003719395.1	s__Streptomyces altiplanensis	89.1044	1436	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	96.26	0.83	0.83	2	-
GCF_018614055.1	s__Streptomyces sp018614055	87.0717	1465	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091725.1	s__Streptomyces sp900091725	83.1759	1229	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001905905.1	s__Streptomyces sp001905905	82.9493	1189	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.31	99.31	0.95	0.95	2	-
GCF_014650555.1	s__Streptomyces goshikiensis	82.4527	1190	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	96.91	0.89	0.81	10	-
GCF_006335115.1	s__Quadrisphaera sp006335115	76.2604	386	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:25,644] [INFO] GTDB search result was written to GCF_005981925.1_ASM598192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:25,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:25,649] [INFO] DFAST_QC result json was written to GCF_005981925.1_ASM598192v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:25,649] [INFO] DFAST_QC completed!
[2024-01-24 14:41:25,649] [INFO] Total running time: 0h2m11s