[2024-01-24 13:31:44,363] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,365] [INFO] DQC Reference Directory: /var/lib/cwl/stg07a1c59f-180a-42b7-b1ae-700346062f00/dqc_reference
[2024-01-24 13:31:45,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,688] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,689] [INFO] Running command: gunzip -c /var/lib/cwl/stgede04e77-5e9f-4350-a15a-72483906a720/GCF_002891435.1_ASM289143v1_genomic.fna.gz | prodigal -d GCF_002891435.1_ASM289143v1_genomic.fna/cds.fna -a GCF_002891435.1_ASM289143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:07,839] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:07,839] [INFO] Task started: HMMsearch
[2024-01-24 13:32:07,839] [INFO] Running command: hmmsearch --tblout GCF_002891435.1_ASM289143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07a1c59f-180a-42b7-b1ae-700346062f00/dqc_reference/reference_markers.hmm GCF_002891435.1_ASM289143v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:08,236] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:08,237] [INFO] Found 6/6 markers.
[2024-01-24 13:32:08,313] [INFO] Query marker FASTA was written to GCF_002891435.1_ASM289143v1_genomic.fna/markers.fasta
[2024-01-24 13:32:08,314] [INFO] Task started: Blastn
[2024-01-24 13:32:08,314] [INFO] Running command: blastn -query GCF_002891435.1_ASM289143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07a1c59f-180a-42b7-b1ae-700346062f00/dqc_reference/reference_markers.fasta -out GCF_002891435.1_ASM289143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:09,867] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:09,877] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:09,878] [INFO] Target genome list was writen to GCF_002891435.1_ASM289143v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:09,894] [INFO] Task started: fastANI
[2024-01-24 13:32:09,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgede04e77-5e9f-4350-a15a-72483906a720/GCF_002891435.1_ASM289143v1_genomic.fna.gz --refList GCF_002891435.1_ASM289143v1_genomic.fna/target_genomes.txt --output GCF_002891435.1_ASM289143v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:46,824] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:46,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07a1c59f-180a-42b7-b1ae-700346062f00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:46,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07a1c59f-180a-42b7-b1ae-700346062f00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:46,844] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:46,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:46,844] [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 cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	100.0	2511	2537	95	conclusive
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	93.6774	1970	2537	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	93.5054	1903	2537	95	below_threshold
Streptomyces hawaiiensis	strain=ATCC 12236	GCA_004803895.1	67305	67305	type	True	92.8521	1949	2537	95	below_threshold
Streptomyces flavovariabilis	strain=NRRL B-16367	GCA_000725785.1	284031	284031	type	True	92.6669	1930	2537	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	92.2716	1908	2537	95	below_threshold
Streptomyces luteogriseus	strain=DSM 40483	GCA_014205055.1	68233	68233	type	True	92.1319	1903	2537	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	92.0199	1744	2537	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	91.6701	1883	2537	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	91.6409	1886	2537	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	91.4264	1672	2537	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	90.5644	1819	2537	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	90.3079	1852	2537	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	85.6737	1705	2537	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.1573	1334	2537	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_014650815.1	68200	68200	type	True	82.2471	1292	2537	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	82.2075	1327	2537	95	below_threshold
Streptomyces alboflavus	strain=NRRL B-2373	GCA_000716675.1	67267	67267	type	True	82.1439	1316	2537	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:46,846] [INFO] DFAST Taxonomy check result was written to GCF_002891435.1_ASM289143v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:46,847] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:46,847] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:46,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07a1c59f-180a-42b7-b1ae-700346062f00/dqc_reference/checkm_data
[2024-01-24 13:32:46,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:46,930] [INFO] Task started: CheckM
[2024-01-24 13:32:46,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002891435.1_ASM289143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002891435.1_ASM289143v1_genomic.fna/checkm_input GCF_002891435.1_ASM289143v1_genomic.fna/checkm_result
[2024-01-24 13:33:57,005] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:57,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:33:57,035] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:57,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:57,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002891435.1_ASM289143v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:57,037] [INFO] Task started: Blastn
[2024-01-24 13:33:57,037] [INFO] Running command: blastn -query GCF_002891435.1_ASM289143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07a1c59f-180a-42b7-b1ae-700346062f00/dqc_reference/reference_markers_gtdb.fasta -out GCF_002891435.1_ASM289143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:59,241] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:59,246] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:59,246] [INFO] Target genome list was writen to GCF_002891435.1_ASM289143v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:59,269] [INFO] Task started: fastANI
[2024-01-24 13:33:59,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgede04e77-5e9f-4350-a15a-72483906a720/GCF_002891435.1_ASM289143v1_genomic.fna.gz --refList GCF_002891435.1_ASM289143v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002891435.1_ASM289143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:30,057] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:30,075] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:34:30,075] [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_001611795.1	s__Streptomyces qaidamensis	93.9844	1979	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3368	N/A	N/A	N/A	N/A	1	-
GCF_014202475.1	s__Streptomyces paradoxus	93.8992	1901	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014204745.1	s__Streptomyces collinus	93.6933	1969	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	-
GCF_000717055.1	s__Streptomyces iakyrus	93.532	1901	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_004803895.1	s__Streptomyces hawaiiensis	92.858	1948	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.39	95.39	0.84	0.84	3	-
GCF_014648995.1	s__Streptomyces massasporeus	92.2903	1905	2537	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	92.1378	1902	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCF_007655005.1	s__Streptomyces tibetensis	91.653	1885	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001280065.1	s__Streptomyces sp001280065	91.3848	1802	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160855.1	s__Streptomyces ferrugineus	85.6775	1707	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267885.1	s__Streptomyces ambofaciens	85.2742	1530	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.23	99.23	0.92	0.92	2	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	83.4889	1411	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_001642995.1	s__Streptomyces jeddahensis	83.1864	1382	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650815.1	s__Streptomyces flavofungini	82.2258	1296	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000716675.1	s__Streptomyces alboflavus	82.1594	1313	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.12	98.24	0.94	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:30,077] [INFO] GTDB search result was written to GCF_002891435.1_ASM289143v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:30,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:30,082] [INFO] DFAST_QC result json was written to GCF_002891435.1_ASM289143v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:30,082] [INFO] DFAST_QC completed!
[2024-01-24 13:34:30,083] [INFO] Total running time: 0h2m46s