[2024-01-25 20:00:20,635] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:20,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:20,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg8774f64d-358c-492a-bb44-4c28b26b3cb0/dqc_reference
[2024-01-25 20:00:21,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:21,835] [INFO] Task started: Prodigal
[2024-01-25 20:00:21,836] [INFO] Running command: gunzip -c /var/lib/cwl/stgc07ee4e9-d8aa-4049-9399-756af42ef1d4/GCF_002078235.1_ASM207823v1_genomic.fna.gz | prodigal -d GCF_002078235.1_ASM207823v1_genomic.fna/cds.fna -a GCF_002078235.1_ASM207823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:40,335] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:40,335] [INFO] Task started: HMMsearch
[2024-01-25 20:00:40,335] [INFO] Running command: hmmsearch --tblout GCF_002078235.1_ASM207823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8774f64d-358c-492a-bb44-4c28b26b3cb0/dqc_reference/reference_markers.hmm GCF_002078235.1_ASM207823v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:40,640] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:40,641] [INFO] Found 6/6 markers.
[2024-01-25 20:00:40,701] [INFO] Query marker FASTA was written to GCF_002078235.1_ASM207823v1_genomic.fna/markers.fasta
[2024-01-25 20:00:40,701] [INFO] Task started: Blastn
[2024-01-25 20:00:40,701] [INFO] Running command: blastn -query GCF_002078235.1_ASM207823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8774f64d-358c-492a-bb44-4c28b26b3cb0/dqc_reference/reference_markers.fasta -out GCF_002078235.1_ASM207823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:42,008] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:42,010] [INFO] Selected 19 target genomes.
[2024-01-25 20:00:42,011] [INFO] Target genome list was writen to GCF_002078235.1_ASM207823v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:42,026] [INFO] Task started: fastANI
[2024-01-25 20:00:42,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07ee4e9-d8aa-4049-9399-756af42ef1d4/GCF_002078235.1_ASM207823v1_genomic.fna.gz --refList GCF_002078235.1_ASM207823v1_genomic.fna/target_genomes.txt --output GCF_002078235.1_ASM207823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:17,134] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:17,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8774f64d-358c-492a-bb44-4c28b26b3cb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:17,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8774f64d-358c-492a-bb44-4c28b26b3cb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:17,146] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:01:17,146] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:01:17,147] [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 viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	100.0	2212	2249	95	conclusive
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	91.7866	1627	2249	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	91.7399	1635	2249	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	89.4553	1528	2249	95	below_threshold
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	89.3551	1529	2249	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	89.1527	1531	2249	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	88.8013	1520	2249	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	88.7281	1536	2249	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	88.389	1583	2249	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.6159	1433	2249	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	86.3421	1478	2249	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	86.2742	1422	2249	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.0241	1282	2249	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.8233	1278	2249	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	81.7221	1086	2249	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	81.5639	1170	2249	95	below_threshold
Streptomyces albulus	strain=JCM 4718	GCA_014650635.1	68570	68570	suspected-type	True	80.8047	1117	2249	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	79.928	892	2249	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	79.8031	992	2249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:17,148] [INFO] DFAST Taxonomy check result was written to GCF_002078235.1_ASM207823v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:17,149] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:17,149] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:17,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8774f64d-358c-492a-bb44-4c28b26b3cb0/dqc_reference/checkm_data
[2024-01-25 20:01:17,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:17,226] [INFO] Task started: CheckM
[2024-01-25 20:01:17,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002078235.1_ASM207823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002078235.1_ASM207823v1_genomic.fna/checkm_input GCF_002078235.1_ASM207823v1_genomic.fna/checkm_result
[2024-01-25 20:02:27,892] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:27,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:27,913] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:27,914] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:27,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002078235.1_ASM207823v1_genomic.fna/markers.fasta)
[2024-01-25 20:02:27,915] [INFO] Task started: Blastn
[2024-01-25 20:02:27,915] [INFO] Running command: blastn -query GCF_002078235.1_ASM207823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8774f64d-358c-492a-bb44-4c28b26b3cb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002078235.1_ASM207823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:30,090] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:30,093] [INFO] Selected 16 target genomes.
[2024-01-25 20:02:30,093] [INFO] Target genome list was writen to GCF_002078235.1_ASM207823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:30,115] [INFO] Task started: fastANI
[2024-01-25 20:02:30,115] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07ee4e9-d8aa-4049-9399-756af42ef1d4/GCF_002078235.1_ASM207823v1_genomic.fna.gz --refList GCF_002078235.1_ASM207823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002078235.1_ASM207823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:01,020] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:01,030] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:01,031] [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_008704515.1	s__Streptomyces viridosporus	96.9967	1725	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.12	0.96	0.94	4	conclusive
GCF_009852415.1	s__Streptomyces sp009852415	91.8467	1653	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	91.7255	1636	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_019049255.1	s__Streptomyces sp019049255	89.4151	1595	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014650015.1	s__Streptomyces griseoloalbus	89.3905	1549	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	99.17	0.94	0.94	3	-
GCF_001905725.1	s__Streptomyces sp001905725	89.336	1612	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721605.1	s__Streptomyces sp000721605	89.196	1548	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312835.1	s__Streptomyces marokkonensis	88.7655	1536	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006782915.1	s__Streptomyces calvus	88.7487	1531	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_014649995.1	s__Streptomyces griseoflavus	88.379	1584	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143855.1	s__Streptomyces sp003143855	88.0672	1563	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
GCF_014534645.1	s__Streptomyces sp014534645	86.3043	1483	2249	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	86.2385	1370	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003270085.1	s__Streptomyces triticisoli	85.7608	1229	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001906585.1	s__Streptomyces kebangsaanensis	85.6426	1399	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373585.1	s__Streptomyces sp000373585	81.0499	1033	2249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:01,033] [INFO] GTDB search result was written to GCF_002078235.1_ASM207823v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:01,034] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:01,037] [INFO] DFAST_QC result json was written to GCF_002078235.1_ASM207823v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:01,037] [INFO] DFAST_QC completed!
[2024-01-25 20:03:01,037] [INFO] Total running time: 0h2m40s