[2024-01-25 18:09:05,808] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:05,810] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:05,810] [INFO] DQC Reference Directory: /var/lib/cwl/stgbba7b844-40b2-4e97-b59e-41648743c0ce/dqc_reference
[2024-01-25 18:09:06,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:06,974] [INFO] Task started: Prodigal
[2024-01-25 18:09:06,974] [INFO] Running command: gunzip -c /var/lib/cwl/stgaaf59e41-e51b-41b7-8b3e-f5e2437ae884/GCF_031593255.1_ASM3159325v1_genomic.fna.gz | prodigal -d GCF_031593255.1_ASM3159325v1_genomic.fna/cds.fna -a GCF_031593255.1_ASM3159325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:31,252] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:31,252] [INFO] Task started: HMMsearch
[2024-01-25 18:09:31,252] [INFO] Running command: hmmsearch --tblout GCF_031593255.1_ASM3159325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbba7b844-40b2-4e97-b59e-41648743c0ce/dqc_reference/reference_markers.hmm GCF_031593255.1_ASM3159325v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:31,575] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:31,576] [INFO] Found 6/6 markers.
[2024-01-25 18:09:31,642] [INFO] Query marker FASTA was written to GCF_031593255.1_ASM3159325v1_genomic.fna/markers.fasta
[2024-01-25 18:09:31,642] [INFO] Task started: Blastn
[2024-01-25 18:09:31,642] [INFO] Running command: blastn -query GCF_031593255.1_ASM3159325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbba7b844-40b2-4e97-b59e-41648743c0ce/dqc_reference/reference_markers.fasta -out GCF_031593255.1_ASM3159325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:32,844] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:32,848] [INFO] Selected 11 target genomes.
[2024-01-25 18:09:32,848] [INFO] Target genome list was writen to GCF_031593255.1_ASM3159325v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:32,852] [INFO] Task started: fastANI
[2024-01-25 18:09:32,852] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaf59e41-e51b-41b7-8b3e-f5e2437ae884/GCF_031593255.1_ASM3159325v1_genomic.fna.gz --refList GCF_031593255.1_ASM3159325v1_genomic.fna/target_genomes.txt --output GCF_031593255.1_ASM3159325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:59,019] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:59,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbba7b844-40b2-4e97-b59e-41648743c0ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:59,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbba7b844-40b2-4e97-b59e-41648743c0ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:59,028] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 18:09:59,028] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:09:59,028] [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 janthinus	strain=JCM 4387	GCA_014649675.1	67308	67308	type	True	99.9775	3107	3150	95	inconclusive
Streptomyces violarus	strain=JCM 4534	GCA_014650255.1	67380	67380	type	True	96.9461	2686	3150	95	inconclusive
Streptomyces violarus	strain=CECT 3237	GCA_014191845.1	67380	67380	type	True	96.9091	2692	3150	95	inconclusive
Streptomyces purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	95.6266	2593	3150	95	inconclusive
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	95.5918	2576	3150	95	inconclusive
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	91.3383	2265	3150	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	90.292	1831	3150	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	89.8657	1934	3150	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.9897	1822	3150	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	83.6974	1915	3150	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_003568675.1	2315329	2315329	type	True	83.6805	1919	3150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:59,029] [INFO] DFAST Taxonomy check result was written to GCF_031593255.1_ASM3159325v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:59,030] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:59,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:59,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbba7b844-40b2-4e97-b59e-41648743c0ce/dqc_reference/checkm_data
[2024-01-25 18:09:59,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:59,115] [INFO] Task started: CheckM
[2024-01-25 18:09:59,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031593255.1_ASM3159325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031593255.1_ASM3159325v1_genomic.fna/checkm_input GCF_031593255.1_ASM3159325v1_genomic.fna/checkm_result
[2024-01-25 18:12:56,389] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:56,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-25 18:12:56,418] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:56,418] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:56,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031593255.1_ASM3159325v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:56,421] [INFO] Task started: Blastn
[2024-01-25 18:12:56,421] [INFO] Running command: blastn -query GCF_031593255.1_ASM3159325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbba7b844-40b2-4e97-b59e-41648743c0ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_031593255.1_ASM3159325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:58,495] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:58,497] [INFO] Selected 24 target genomes.
[2024-01-25 18:12:58,498] [INFO] Target genome list was writen to GCF_031593255.1_ASM3159325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:58,514] [INFO] Task started: fastANI
[2024-01-25 18:12:58,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaf59e41-e51b-41b7-8b3e-f5e2437ae884/GCF_031593255.1_ASM3159325v1_genomic.fna.gz --refList GCF_031593255.1_ASM3159325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031593255.1_ASM3159325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:57,395] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:57,409] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:57,409] [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
GCA_000715635.1	s__Streptomyces violaceus	97.3114	2643	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.39	95.19	0.85	0.83	5	conclusive
GCF_018604545.1	s__Streptomyces sp018604545	94.0379	2462	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008705135.1	s__Streptomyces coeruleorubidus	91.627	2489	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	-
GCF_900236475.1	s__Streptomyces chartreusis_D	91.5192	2398	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_002148965.1	s__Streptomyces swartbergensis	91.3942	2016	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651035.1	s__Streptomyces lomondensis	91.3369	2281	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150735.1	s__Streptomyces africanus	91.2973	2065	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018195615.1	s__Streptomyces tuirus_A	91.1746	2307	3150	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	91.1113	2282	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000696115.1	s__Streptomyces olindensis	90.7941	2319	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648995.1	s__Streptomyces massasporeus	90.6591	2344	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCF_014205055.1	s__Streptomyces luteogriseus	90.5798	2284	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCF_014651075.1	s__Streptomyces djakartensis	90.251	2041	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685355.1	s__Streptomyces lincolnensis	86.0002	2189	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.95	3	-
GCF_014648815.1	s__Streptomyces flaveolus	85.8384	1783	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042075.1	s__Streptomyces sp008042075	85.7913	2058	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015712165.1	s__Streptomyces spinoverrucosus_A	85.7628	1935	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	85.6555	1843	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248315.1	s__Streptomyces sp003248315	85.5582	1726	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282115.1	s__Streptomyces sp001282115	85.5389	1714	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	0.95	0.95	2	-
GCF_001746295.1	s__Streptomyces sp001746295	85.2978	2085	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362785.1	s__Streptomyces sp013362785	85.2021	1569	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280195.1	s__Streptomyces galbus	84.6277	1709	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_005768555.2	s__Streptomyces sporangiiformans	83.6897	1918	3150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.93	95.85	0.91	0.82	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:57,411] [INFO] GTDB search result was written to GCF_031593255.1_ASM3159325v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:57,412] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:57,415] [INFO] DFAST_QC result json was written to GCF_031593255.1_ASM3159325v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:57,415] [INFO] DFAST_QC completed!
[2024-01-25 18:13:57,415] [INFO] Total running time: 0h4m52s