[2024-01-25 18:03:05,469] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:05,470] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:05,470] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb077b5f-9551-41bc-9a01-60c585639b39/dqc_reference
[2024-01-25 18:03:06,589] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:06,589] [INFO] Task started: Prodigal
[2024-01-25 18:03:06,589] [INFO] Running command: gunzip -c /var/lib/cwl/stgc67324d7-6c5d-47c7-880d-27b3c801ea39/GCF_014655595.1_ASM1465559v1_genomic.fna.gz | prodigal -d GCF_014655595.1_ASM1465559v1_genomic.fna/cds.fna -a GCF_014655595.1_ASM1465559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:25,641] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:25,641] [INFO] Task started: HMMsearch
[2024-01-25 18:03:25,641] [INFO] Running command: hmmsearch --tblout GCF_014655595.1_ASM1465559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb077b5f-9551-41bc-9a01-60c585639b39/dqc_reference/reference_markers.hmm GCF_014655595.1_ASM1465559v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:25,921] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:25,922] [INFO] Found 6/6 markers.
[2024-01-25 18:03:25,979] [INFO] Query marker FASTA was written to GCF_014655595.1_ASM1465559v1_genomic.fna/markers.fasta
[2024-01-25 18:03:25,980] [INFO] Task started: Blastn
[2024-01-25 18:03:25,980] [INFO] Running command: blastn -query GCF_014655595.1_ASM1465559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb077b5f-9551-41bc-9a01-60c585639b39/dqc_reference/reference_markers.fasta -out GCF_014655595.1_ASM1465559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:27,226] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:27,231] [INFO] Selected 21 target genomes.
[2024-01-25 18:03:27,231] [INFO] Target genome list was writen to GCF_014655595.1_ASM1465559v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:27,251] [INFO] Task started: fastANI
[2024-01-25 18:03:27,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgc67324d7-6c5d-47c7-880d-27b3c801ea39/GCF_014655595.1_ASM1465559v1_genomic.fna.gz --refList GCF_014655595.1_ASM1465559v1_genomic.fna/target_genomes.txt --output GCF_014655595.1_ASM1465559v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:07,271] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:07,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb077b5f-9551-41bc-9a01-60c585639b39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:07,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb077b5f-9551-41bc-9a01-60c585639b39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:07,284] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:04:07,284] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:07,285] [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=JCM 4580	GCA_014655595.1	51201	51201	type	True	100.0	2440	2440	95	conclusive
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	99.9797	2410	2440	95	conclusive
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	87.1241	1426	2440	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	86.8221	1569	2440	95	below_threshold
Streptomyces netropsis	strain=JCM 4063	GCA_014648835.1	55404	55404	type	True	85.9064	1635	2440	95	below_threshold
Streptomyces netropsis	strain=CECT 3265	GCA_014203545.1	55404	55404	type	True	85.7901	1673	2440	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	85.5652	1598	2440	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	85.5566	1671	2440	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	85.494	1590	2440	95	below_threshold
Streptomyces syringium	strain=DSM 41480	GCA_017876625.1	76729	76729	type	True	85.4481	1632	2440	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	85.2506	1629	2440	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	85.2467	1568	2440	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	85.1405	1578	2440	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	83.9962	1375	2440	95	below_threshold
Streptomyces orinoci	strain=NRRL B-3379	GCA_003121295.1	67339	67339	type	True	83.089	1357	2440	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.472	1092	2440	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.0602	1221	2440	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.002	1200	2440	95	below_threshold
Streptomyces gougerotii	strain=JCM 4136	GCA_014648955.1	53448	53448	suspected-type	True	80.9628	1112	2440	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	80.0158	1112	2440	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	76.7934	574	2440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:07,286] [INFO] DFAST Taxonomy check result was written to GCF_014655595.1_ASM1465559v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:07,286] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:07,286] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:07,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb077b5f-9551-41bc-9a01-60c585639b39/dqc_reference/checkm_data
[2024-01-25 18:04:07,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:07,353] [INFO] Task started: CheckM
[2024-01-25 18:04:07,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014655595.1_ASM1465559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014655595.1_ASM1465559v1_genomic.fna/checkm_input GCF_014655595.1_ASM1465559v1_genomic.fna/checkm_result
[2024-01-25 18:05:39,348] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:39,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:39,377] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:39,377] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:39,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014655595.1_ASM1465559v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:39,378] [INFO] Task started: Blastn
[2024-01-25 18:05:39,378] [INFO] Running command: blastn -query GCF_014655595.1_ASM1465559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb077b5f-9551-41bc-9a01-60c585639b39/dqc_reference/reference_markers_gtdb.fasta -out GCF_014655595.1_ASM1465559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:41,540] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:41,545] [INFO] Selected 13 target genomes.
[2024-01-25 18:05:41,546] [INFO] Target genome list was writen to GCF_014655595.1_ASM1465559v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:41,566] [INFO] Task started: fastANI
[2024-01-25 18:05:41,566] [INFO] Running command: fastANI --query /var/lib/cwl/stgc67324d7-6c5d-47c7-880d-27b3c801ea39/GCF_014655595.1_ASM1465559v1_genomic.fna.gz --refList GCF_014655595.1_ASM1465559v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014655595.1_ASM1465559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:07,551] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:07,560] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:07,560] [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	100.0	2440	2440	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	93.7584	2039	2440	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	87.6507	1685	2440	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	87.5213	1640	2440	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	87.145	1424	2440	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	87.0262	1592	2440	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	86.7755	1576	2440	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	85.8131	1670	2440	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	85.5741	1667	2440	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	85.4371	1633	2440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.60	0.98	0.98	2	-
GCF_003391135.1	s__Streptomyces olivoreticuli	85.1018	1551	2440	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	81.3182	1149	2440	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	80.0304	1110	2440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:07,562] [INFO] GTDB search result was written to GCF_014655595.1_ASM1465559v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:07,563] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:07,566] [INFO] DFAST_QC result json was written to GCF_014655595.1_ASM1465559v1_genomic.fna/dqc_result.json
[2024-01-25 18:06:07,566] [INFO] DFAST_QC completed!
[2024-01-25 18:06:07,566] [INFO] Total running time: 0h3m2s