[2024-01-24 13:37:25,951] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:25,952] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:25,952] [INFO] DQC Reference Directory: /var/lib/cwl/stg727e0a60-d0d9-48ae-a1d5-a7b784228002/dqc_reference
[2024-01-24 13:37:27,230] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:27,230] [INFO] Task started: Prodigal
[2024-01-24 13:37:27,231] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c50085b-637d-4d69-9095-216295d208ee/GCF_014650155.1_ASM1465015v1_genomic.fna.gz | prodigal -d GCF_014650155.1_ASM1465015v1_genomic.fna/cds.fna -a GCF_014650155.1_ASM1465015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:50,944] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:50,944] [INFO] Task started: HMMsearch
[2024-01-24 13:37:50,945] [INFO] Running command: hmmsearch --tblout GCF_014650155.1_ASM1465015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg727e0a60-d0d9-48ae-a1d5-a7b784228002/dqc_reference/reference_markers.hmm GCF_014650155.1_ASM1465015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:51,324] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:51,325] [INFO] Found 6/6 markers.
[2024-01-24 13:37:51,400] [INFO] Query marker FASTA was written to GCF_014650155.1_ASM1465015v1_genomic.fna/markers.fasta
[2024-01-24 13:37:51,400] [INFO] Task started: Blastn
[2024-01-24 13:37:51,401] [INFO] Running command: blastn -query GCF_014650155.1_ASM1465015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg727e0a60-d0d9-48ae-a1d5-a7b784228002/dqc_reference/reference_markers.fasta -out GCF_014650155.1_ASM1465015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:52,643] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:52,646] [INFO] Selected 16 target genomes.
[2024-01-24 13:37:52,646] [INFO] Target genome list was writen to GCF_014650155.1_ASM1465015v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:52,657] [INFO] Task started: fastANI
[2024-01-24 13:37:52,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c50085b-637d-4d69-9095-216295d208ee/GCF_014650155.1_ASM1465015v1_genomic.fna.gz --refList GCF_014650155.1_ASM1465015v1_genomic.fna/target_genomes.txt --output GCF_014650155.1_ASM1465015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:27,481] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:27,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg727e0a60-d0d9-48ae-a1d5-a7b784228002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:27,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg727e0a60-d0d9-48ae-a1d5-a7b784228002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:27,491] [INFO] Found 16 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:38:27,491] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:38:27,492] [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 purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	100.0	3118	3120	95	inconclusive
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	99.9865	3079	3120	95	inconclusive
Streptomyces violarus	strain=JCM 4534	GCA_014650255.1	67380	67380	type	True	95.7256	2618	3120	95	inconclusive
Streptomyces violarus	strain=CECT 3237	GCA_014191845.1	67380	67380	type	True	95.7128	2622	3120	95	inconclusive
Streptomyces janthinus	strain=JCM 4387	GCA_014649675.1	67308	67308	type	True	95.5771	2595	3120	95	inconclusive
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	91.3578	2280	3120	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	90.7782	2368	3120	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	90.6841	2317	3120	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	90.2721	2294	3120	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	90.2547	1827	3120	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	90.0032	1926	3120	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.4913	1771	3120	95	below_threshold
Streptomyces echinoruber	strain=JCM 5016	GCA_014651135.1	68898	68898	type	True	84.3864	1612	3120	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.3398	1076	3120	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	78.3688	1046	3120	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	76.5704	574	3120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:27,493] [INFO] DFAST Taxonomy check result was written to GCF_014650155.1_ASM1465015v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:27,493] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:27,493] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:27,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg727e0a60-d0d9-48ae-a1d5-a7b784228002/dqc_reference/checkm_data
[2024-01-24 13:38:27,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:27,578] [INFO] Task started: CheckM
[2024-01-24 13:38:27,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650155.1_ASM1465015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650155.1_ASM1465015v1_genomic.fna/checkm_input GCF_014650155.1_ASM1465015v1_genomic.fna/checkm_result
[2024-01-24 13:40:36,858] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:36,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:36,889] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:36,890] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:36,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650155.1_ASM1465015v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:36,890] [INFO] Task started: Blastn
[2024-01-24 13:40:36,890] [INFO] Running command: blastn -query GCF_014650155.1_ASM1465015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg727e0a60-d0d9-48ae-a1d5-a7b784228002/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650155.1_ASM1465015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:38,851] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:38,854] [INFO] Selected 25 target genomes.
[2024-01-24 13:40:38,854] [INFO] Target genome list was writen to GCF_014650155.1_ASM1465015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:38,928] [INFO] Task started: fastANI
[2024-01-24 13:40:38,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c50085b-637d-4d69-9095-216295d208ee/GCF_014650155.1_ASM1465015v1_genomic.fna.gz --refList GCF_014650155.1_ASM1465015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650155.1_ASM1465015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:38,044] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:38,059] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:38,059] [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	95.1211	2575	3120	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	94.5904	2536	3120	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	91.6747	2232	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900236475.1	s__Streptomyces chartreusis_D	91.5733	2345	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCA_018195615.1	s__Streptomyces tuirus_A	91.3124	2268	3120	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	91.2091	2038	3120	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	91.0447	2301	3120	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	90.8541	2304	3120	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	90.7715	2369	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCA_014204745.1	s__Streptomyces collinus	90.6986	2318	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	-
GCF_014205055.1	s__Streptomyces luteogriseus	90.5357	2285	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCF_000717875.1	s__Streptomyces sp000717875	90.4539	2108	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.70	99.70	0.96	0.96	2	-
GCF_007655005.1	s__Streptomyces tibetensis	90.2736	2294	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014651075.1	s__Streptomyces djakartensis	90.245	2015	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028635.1	s__Streptomyces cyaneus	86.2259	2173	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	86.0042	1856	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514235.1	s__Streptomyces caeruleatus	85.9295	2152	3120	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	85.8609	2068	3120	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	85.79	2083	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671715.1	s__Streptomyces sp003671715	85.6653	1829	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCF_001282115.1	s__Streptomyces sp001282115	85.6208	1751	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	0.95	0.95	2	-
GCA_003248315.1	s__Streptomyces sp003248315	85.4267	1757	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650435.1	s__Streptomyces tendae	85.2108	1823	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_003143855.1	s__Streptomyces sp003143855	85.1652	1691	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
GCA_014649295.1	s__Streptomyces libani_A	84.4948	1728	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:38,060] [INFO] GTDB search result was written to GCF_014650155.1_ASM1465015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:38,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:38,064] [INFO] DFAST_QC result json was written to GCF_014650155.1_ASM1465015v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:38,064] [INFO] DFAST_QC completed!
[2024-01-24 13:41:38,064] [INFO] Total running time: 0h4m12s