[2024-01-24 15:26:54,795] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:54,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:54,799] [INFO] DQC Reference Directory: /var/lib/cwl/stg4101a1c9-9d2f-4d23-9f93-7cecd5d0f62e/dqc_reference
[2024-01-24 15:26:56,357] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,358] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg25fbd3fd-b175-4072-8d43-86d689277229/GCF_020093395.1_ASM2009339v1_genomic.fna.gz | prodigal -d GCF_020093395.1_ASM2009339v1_genomic.fna/cds.fna -a GCF_020093395.1_ASM2009339v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:17,057] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:17,057] [INFO] Task started: HMMsearch
[2024-01-24 15:27:17,057] [INFO] Running command: hmmsearch --tblout GCF_020093395.1_ASM2009339v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4101a1c9-9d2f-4d23-9f93-7cecd5d0f62e/dqc_reference/reference_markers.hmm GCF_020093395.1_ASM2009339v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:17,433] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:17,434] [INFO] Found 6/6 markers.
[2024-01-24 15:27:17,503] [INFO] Query marker FASTA was written to GCF_020093395.1_ASM2009339v1_genomic.fna/markers.fasta
[2024-01-24 15:27:17,504] [INFO] Task started: Blastn
[2024-01-24 15:27:17,504] [INFO] Running command: blastn -query GCF_020093395.1_ASM2009339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4101a1c9-9d2f-4d23-9f93-7cecd5d0f62e/dqc_reference/reference_markers.fasta -out GCF_020093395.1_ASM2009339v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:18,845] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:18,848] [INFO] Selected 22 target genomes.
[2024-01-24 15:27:18,849] [INFO] Target genome list was writen to GCF_020093395.1_ASM2009339v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:18,858] [INFO] Task started: fastANI
[2024-01-24 15:27:18,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg25fbd3fd-b175-4072-8d43-86d689277229/GCF_020093395.1_ASM2009339v1_genomic.fna.gz --refList GCF_020093395.1_ASM2009339v1_genomic.fna/target_genomes.txt --output GCF_020093395.1_ASM2009339v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:59,123] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:59,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4101a1c9-9d2f-4d23-9f93-7cecd5d0f62e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:59,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4101a1c9-9d2f-4d23-9f93-7cecd5d0f62e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:59,140] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:59,141] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:59,141] [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 griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	100.0	2425	2429	95	conclusive
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	99.9871	2417	2429	95	conclusive
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	87.1274	1419	2429	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	86.7221	1588	2429	95	below_threshold
Streptomyces netropsis	strain=JCM 4063	GCA_014648835.1	55404	55404	type	True	85.85	1631	2429	95	below_threshold
Streptomyces netropsis	strain=CECT 3265	GCA_014203545.1	55404	55404	type	True	85.7993	1663	2429	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	85.6082	1665	2429	95	below_threshold
Streptomyces syringium	strain=DSM 41480	GCA_017876625.1	76729	76729	type	True	85.5337	1599	2429	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	85.5143	1629	2429	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	85.4565	1586	2429	95	below_threshold
Streptomyces eurocidicus	strain=CECT 3259	GCA_014203505.1	66423	66423	type	True	85.2962	1569	2429	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	85.2465	1621	2429	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	85.1913	1594	2429	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	85.1799	1570	2429	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	83.9674	1392	2429	95	below_threshold
Streptomyces orinoci	strain=NRRL B-3379	GCA_003121295.1	67339	67339	type	True	83.1278	1335	2429	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.3585	1107	2429	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.1126	1229	2429	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.051	1183	2429	95	below_threshold
Streptomyces gougerotii	strain=JCM 4136	GCA_014648955.1	53448	53448	suspected-type	True	80.86	1114	2429	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	80.0092	1108	2429	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	76.8514	586	2429	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:59,142] [INFO] DFAST Taxonomy check result was written to GCF_020093395.1_ASM2009339v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:59,143] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:59,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:59,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4101a1c9-9d2f-4d23-9f93-7cecd5d0f62e/dqc_reference/checkm_data
[2024-01-24 15:27:59,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:59,208] [INFO] Task started: CheckM
[2024-01-24 15:27:59,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020093395.1_ASM2009339v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020093395.1_ASM2009339v1_genomic.fna/checkm_input GCF_020093395.1_ASM2009339v1_genomic.fna/checkm_result
[2024-01-24 15:29:31,542] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:31,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:31,565] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:31,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:31,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020093395.1_ASM2009339v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:31,566] [INFO] Task started: Blastn
[2024-01-24 15:29:31,566] [INFO] Running command: blastn -query GCF_020093395.1_ASM2009339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4101a1c9-9d2f-4d23-9f93-7cecd5d0f62e/dqc_reference/reference_markers_gtdb.fasta -out GCF_020093395.1_ASM2009339v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:33,726] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:33,729] [INFO] Selected 15 target genomes.
[2024-01-24 15:29:33,730] [INFO] Target genome list was writen to GCF_020093395.1_ASM2009339v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:33,740] [INFO] Task started: fastANI
[2024-01-24 15:29:33,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg25fbd3fd-b175-4072-8d43-86d689277229/GCF_020093395.1_ASM2009339v1_genomic.fna.gz --refList GCF_020093395.1_ASM2009339v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020093395.1_ASM2009339v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:02,271] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:02,283] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:30:02,284] [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_014655595.1	s__Streptomyces griseocarneus	99.9871	2417	2429	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_017349075.1	s__Streptomyces triculaminicus_A	93.803	2025	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.73	0.98	0.98	3	-
GCF_014650495.1	s__Streptomyces cinnamoneus	87.779	1681	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715685.1	s__Streptomyces lilacinus	87.5326	1631	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	87.1622	1416	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939475.1	s__Streptomyces cinnamoneus_A	87.0135	1585	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014648775.1	s__Streptomyces abikoensis	86.7165	1589	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.57	96.57	0.89	0.89	2	-
GCF_014203545.1	s__Streptomyces netropsis	85.8294	1658	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001445655.1	s__Streptomyces roseifaciens	85.6186	1663	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.88	0.88	2	-
GCF_017876625.1	s__Streptomyces syringium	85.5031	1604	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.60	0.98	0.98	2	-
GCF_002286695.1	s__Streptomyces albireticuli	85.35	1399	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002891295.1	s__Streptomyces eurocidicus	85.1926	1593	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	3	-
GCF_003391135.1	s__Streptomyces olivoreticuli	85.1449	1538	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278075.1	s__Streptomyces pristinaespiralis	81.2993	1160	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
GCF_016918855.1	s__Streptomyces acididurans	80.048	1101	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:02,285] [INFO] GTDB search result was written to GCF_020093395.1_ASM2009339v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:02,286] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:02,291] [INFO] DFAST_QC result json was written to GCF_020093395.1_ASM2009339v1_genomic.fna/dqc_result.json
[2024-01-24 15:30:02,291] [INFO] DFAST_QC completed!
[2024-01-24 15:30:02,291] [INFO] Total running time: 0h3m7s