[2024-01-25 19:07:20,806] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:20,808] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:20,808] [INFO] DQC Reference Directory: /var/lib/cwl/stgebefb5ab-03a4-46bc-aca2-2edd77734f11/dqc_reference
[2024-01-25 19:07:21,947] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:21,947] [INFO] Task started: Prodigal
[2024-01-25 19:07:21,948] [INFO] Running command: gunzip -c /var/lib/cwl/stg94aee79c-d18b-44f3-9a3f-eb264f6475ba/GCF_003112595.1_ASM311259v1_genomic.fna.gz | prodigal -d GCF_003112595.1_ASM311259v1_genomic.fna/cds.fna -a GCF_003112595.1_ASM311259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:42,563] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:42,563] [INFO] Task started: HMMsearch
[2024-01-25 19:07:42,563] [INFO] Running command: hmmsearch --tblout GCF_003112595.1_ASM311259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebefb5ab-03a4-46bc-aca2-2edd77734f11/dqc_reference/reference_markers.hmm GCF_003112595.1_ASM311259v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:42,910] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:42,911] [INFO] Found 6/6 markers.
[2024-01-25 19:07:42,979] [INFO] Query marker FASTA was written to GCF_003112595.1_ASM311259v1_genomic.fna/markers.fasta
[2024-01-25 19:07:42,979] [INFO] Task started: Blastn
[2024-01-25 19:07:42,979] [INFO] Running command: blastn -query GCF_003112595.1_ASM311259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebefb5ab-03a4-46bc-aca2-2edd77734f11/dqc_reference/reference_markers.fasta -out GCF_003112595.1_ASM311259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:44,270] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:44,273] [INFO] Selected 17 target genomes.
[2024-01-25 19:07:44,273] [INFO] Target genome list was writen to GCF_003112595.1_ASM311259v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:44,280] [INFO] Task started: fastANI
[2024-01-25 19:07:44,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg94aee79c-d18b-44f3-9a3f-eb264f6475ba/GCF_003112595.1_ASM311259v1_genomic.fna.gz --refList GCF_003112595.1_ASM311259v1_genomic.fna/target_genomes.txt --output GCF_003112595.1_ASM311259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:21,807] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:21,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebefb5ab-03a4-46bc-aca2-2edd77734f11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:21,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebefb5ab-03a4-46bc-aca2-2edd77734f11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:21,821] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:08:21,821] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:08:21,822] [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 rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	100.0	2809	2810	95	inconclusive
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	96.926	2460	2810	95	inconclusive
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	94.1186	2313	2810	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	93.4293	2205	2810	95	below_threshold
Streptomyces violaceorubidus	strain=NRRL B-16381	GCA_000717995.1	284042	284042	type	True	93.1249	2028	2810	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	92.0438	2105	2810	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	89.098	1909	2810	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.8303	1919	2810	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.0143	1515	2810	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.5851	1755	2810	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.2442	1455	2810	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.2253	1614	2810	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	81.729	1458	2810	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	79.9698	1253	2810	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	79.8561	1200	2810	95	below_threshold
Streptomyces sulphureus	strain=DSM 40104	GCA_000381025.1	47758	47758	type	True	78.9378	985	2810	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	76.4933	866	2810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:21,823] [INFO] DFAST Taxonomy check result was written to GCF_003112595.1_ASM311259v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:21,823] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:21,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:21,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebefb5ab-03a4-46bc-aca2-2edd77734f11/dqc_reference/checkm_data
[2024-01-25 19:08:21,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:21,900] [INFO] Task started: CheckM
[2024-01-25 19:08:21,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003112595.1_ASM311259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003112595.1_ASM311259v1_genomic.fna/checkm_input GCF_003112595.1_ASM311259v1_genomic.fna/checkm_result
[2024-01-25 19:10:22,791] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:22,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:22,815] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:22,816] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:22,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003112595.1_ASM311259v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:22,818] [INFO] Task started: Blastn
[2024-01-25 19:10:22,818] [INFO] Running command: blastn -query GCF_003112595.1_ASM311259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebefb5ab-03a4-46bc-aca2-2edd77734f11/dqc_reference/reference_markers_gtdb.fasta -out GCF_003112595.1_ASM311259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:24,939] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:24,941] [INFO] Selected 15 target genomes.
[2024-01-25 19:10:24,942] [INFO] Target genome list was writen to GCF_003112595.1_ASM311259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:24,972] [INFO] Task started: fastANI
[2024-01-25 19:10:24,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg94aee79c-d18b-44f3-9a3f-eb264f6475ba/GCF_003112595.1_ASM311259v1_genomic.fna.gz --refList GCF_003112595.1_ASM311259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003112595.1_ASM311259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:59,198] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:59,208] [INFO] Found 15 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 19:10:59,209] [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_003112595.1	s__Streptomyces rubrogriseus	100.0	2809	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	inconclusive
GCF_014651155.1	s__Streptomyces anthocyanicus	96.9293	2459	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	99.40	98.26	0.96	0.83	31	inconclusive
GCF_003369795.1	s__Streptomyces sp003369795	95.3282	2148	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3499	N/A	N/A	N/A	N/A	1	-
GCF_014650435.1	s__Streptomyces tendae	94.1055	2313	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_002939385.1	s__Streptomyces sp002939385	93.676	2156	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCA_000720845.1	s__Streptomyces sp000720845	93.3833	2237	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717995.1	s__Streptomyces violaceorubidus	93.1159	2029	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112555.1	s__Streptomyces coelicoflavus	92.8043	2224	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_000772045.1	s__Streptomyces sp000772045	92.6721	2180	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	-
GCF_003112575.1	s__Streptomyces ardesiacus	92.0186	2109	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_004364245.1	s__Streptomyces sp004364245	91.9446	2085	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009862265.1	s__Streptomyces sp009862265	85.4843	1542	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049245.1	s__Streptomyces sp019049245	84.8947	1737	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002291145.1	s__Streptomyces sp002291145	84.8085	1703	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203845.1	s__Streptomyces scabiei_E	83.3945	1655	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:59,210] [INFO] GTDB search result was written to GCF_003112595.1_ASM311259v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:59,210] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:59,214] [INFO] DFAST_QC result json was written to GCF_003112595.1_ASM311259v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:59,214] [INFO] DFAST_QC completed!
[2024-01-25 19:10:59,214] [INFO] Total running time: 0h3m38s