[2024-01-24 15:02:18,890] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:18,894] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:18,894] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e669b97-5fdd-4c95-b48a-14e07e7400f1/dqc_reference
[2024-01-24 15:02:20,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:20,835] [INFO] Task started: Prodigal
[2024-01-24 15:02:20,835] [INFO] Running command: gunzip -c /var/lib/cwl/stgc750554e-4c35-42ef-b0f3-dff6bd2ded55/GCF_008705135.1_ASM870513v1_genomic.fna.gz | prodigal -d GCF_008705135.1_ASM870513v1_genomic.fna/cds.fna -a GCF_008705135.1_ASM870513v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:49,630] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:49,631] [INFO] Task started: HMMsearch
[2024-01-24 15:02:49,631] [INFO] Running command: hmmsearch --tblout GCF_008705135.1_ASM870513v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e669b97-5fdd-4c95-b48a-14e07e7400f1/dqc_reference/reference_markers.hmm GCF_008705135.1_ASM870513v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:50,038] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:50,039] [INFO] Found 6/6 markers.
[2024-01-24 15:02:50,131] [INFO] Query marker FASTA was written to GCF_008705135.1_ASM870513v1_genomic.fna/markers.fasta
[2024-01-24 15:02:50,132] [INFO] Task started: Blastn
[2024-01-24 15:02:50,132] [INFO] Running command: blastn -query GCF_008705135.1_ASM870513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e669b97-5fdd-4c95-b48a-14e07e7400f1/dqc_reference/reference_markers.fasta -out GCF_008705135.1_ASM870513v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:51,560] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:51,563] [INFO] Selected 14 target genomes.
[2024-01-24 15:02:51,564] [INFO] Target genome list was writen to GCF_008705135.1_ASM870513v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:51,573] [INFO] Task started: fastANI
[2024-01-24 15:02:51,573] [INFO] Running command: fastANI --query /var/lib/cwl/stgc750554e-4c35-42ef-b0f3-dff6bd2ded55/GCF_008705135.1_ASM870513v1_genomic.fna.gz --refList GCF_008705135.1_ASM870513v1_genomic.fna/target_genomes.txt --output GCF_008705135.1_ASM870513v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:23,745] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:23,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e669b97-5fdd-4c95-b48a-14e07e7400f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:23,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e669b97-5fdd-4c95-b48a-14e07e7400f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:23,757] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:23,757] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:23,757] [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 coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	100.0	3111	3111	95	conclusive
Streptomyces coeruleorubidus	strain=JCM 4359	GCA_014649455.1	116188	116188	suspected-type	True	99.9808	3070	3111	95	conclusive
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	94.9719	2128	3111	95	below_threshold
Streptomyces azureus	strain=ATCC 14921	GCA_001270025.1	146537	146537	type	True	94.9136	2292	3111	95	below_threshold
Streptomyces caelestis	strain=DSM 40084	GCA_014205255.1	36816	36816	type	True	93.8615	2376	3111	95	below_threshold
Streptomyces caelestis	strain=JCM 4566	GCA_014650295.1	36816	36816	type	True	93.8062	2347	3111	95	below_threshold
Streptomyces africanus	strain=NRRL B-24243	GCA_002150735.1	231024	231024	type	True	93.4069	2128	3111	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	91.7407	2298	3111	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	91.3963	2414	3111	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	90.3381	2088	3111	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	90.2743	1825	3111	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	89.9363	1949	3111	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.5064	1544	3111	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	75.0003	168	3111	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:23,759] [INFO] DFAST Taxonomy check result was written to GCF_008705135.1_ASM870513v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:23,760] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:23,760] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:23,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e669b97-5fdd-4c95-b48a-14e07e7400f1/dqc_reference/checkm_data
[2024-01-24 15:03:23,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:23,849] [INFO] Task started: CheckM
[2024-01-24 15:03:23,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008705135.1_ASM870513v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008705135.1_ASM870513v1_genomic.fna/checkm_input GCF_008705135.1_ASM870513v1_genomic.fna/checkm_result
[2024-01-24 15:06:08,675] [INFO] Task succeeded: CheckM
[2024-01-24 15:06:08,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:06:08,703] [INFO] ===== Completeness check finished =====
[2024-01-24 15:06:08,703] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:06:08,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008705135.1_ASM870513v1_genomic.fna/markers.fasta)
[2024-01-24 15:06:08,704] [INFO] Task started: Blastn
[2024-01-24 15:06:08,704] [INFO] Running command: blastn -query GCF_008705135.1_ASM870513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e669b97-5fdd-4c95-b48a-14e07e7400f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_008705135.1_ASM870513v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:10,937] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:10,942] [INFO] Selected 13 target genomes.
[2024-01-24 15:06:10,942] [INFO] Target genome list was writen to GCF_008705135.1_ASM870513v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:06:10,955] [INFO] Task started: fastANI
[2024-01-24 15:06:10,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgc750554e-4c35-42ef-b0f3-dff6bd2ded55/GCF_008705135.1_ASM870513v1_genomic.fna.gz --refList GCF_008705135.1_ASM870513v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008705135.1_ASM870513v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:06:44,025] [INFO] Task succeeded: fastANI
[2024-01-24 15:06:44,049] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:06:44,049] [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_008705135.1	s__Streptomyces coeruleorubidus	100.0	3111	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	conclusive
GCF_002148965.1	s__Streptomyces swartbergensis	94.9804	2127	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000415505.1	s__Streptomyces afghaniensis	93.9238	2311	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205255.1	s__Streptomyces caelestis	93.8484	2377	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900236475.1	s__Streptomyces chartreusis_D	93.6574	2406	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_002150735.1	s__Streptomyces africanus	93.4031	2129	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158955.1	s__Streptomyces viridochromogenes_B	90.9943	2246	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648815.1	s__Streptomyces flaveolus	85.8312	1796	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364215.1	s__Streptomyces sp004364215	85.7825	2097	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717595.1	s__Streptomyces flavochromogenes	81.3938	1450	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	81.1361	1104	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349075.1	s__Streptomyces triculaminicus_A	80.8014	1241	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.73	0.98	0.98	3	-
GCF_009176265.1	s__Streptomyces angustmyceticus	80.7959	1327	3111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:06:44,052] [INFO] GTDB search result was written to GCF_008705135.1_ASM870513v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:06:44,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:06:44,059] [INFO] DFAST_QC result json was written to GCF_008705135.1_ASM870513v1_genomic.fna/dqc_result.json
[2024-01-24 15:06:44,059] [INFO] DFAST_QC completed!
[2024-01-24 15:06:44,059] [INFO] Total running time: 0h4m25s