[2024-01-25 19:55:50,722] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:50,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:50,724] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe5e052d-59f4-4d77-bd26-304aaf282d68/dqc_reference
[2024-01-25 19:55:51,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:51,949] [INFO] Task started: Prodigal
[2024-01-25 19:55:51,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c982572-c0e3-4f7d-992e-c44ce7fa61ec/GCF_023498005.1_ASM2349800v1_genomic.fna.gz | prodigal -d GCF_023498005.1_ASM2349800v1_genomic.fna/cds.fna -a GCF_023498005.1_ASM2349800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:22,380] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:22,381] [INFO] Task started: HMMsearch
[2024-01-25 19:56:22,381] [INFO] Running command: hmmsearch --tblout GCF_023498005.1_ASM2349800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe5e052d-59f4-4d77-bd26-304aaf282d68/dqc_reference/reference_markers.hmm GCF_023498005.1_ASM2349800v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:22,857] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:22,858] [INFO] Found 6/6 markers.
[2024-01-25 19:56:22,939] [INFO] Query marker FASTA was written to GCF_023498005.1_ASM2349800v1_genomic.fna/markers.fasta
[2024-01-25 19:56:22,939] [INFO] Task started: Blastn
[2024-01-25 19:56:22,939] [INFO] Running command: blastn -query GCF_023498005.1_ASM2349800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe5e052d-59f4-4d77-bd26-304aaf282d68/dqc_reference/reference_markers.fasta -out GCF_023498005.1_ASM2349800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:24,348] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:24,351] [INFO] Selected 20 target genomes.
[2024-01-25 19:56:24,351] [INFO] Target genome list was writen to GCF_023498005.1_ASM2349800v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:24,369] [INFO] Task started: fastANI
[2024-01-25 19:56:24,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c982572-c0e3-4f7d-992e-c44ce7fa61ec/GCF_023498005.1_ASM2349800v1_genomic.fna.gz --refList GCF_023498005.1_ASM2349800v1_genomic.fna/target_genomes.txt --output GCF_023498005.1_ASM2349800v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:10,838] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:10,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe5e052d-59f4-4d77-bd26-304aaf282d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:10,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe5e052d-59f4-4d77-bd26-304aaf282d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:10,850] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:10,850] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:10,850] [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 durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	100.0	3287	3287	95	conclusive
Streptomyces longisporoflavus	strain=JCM 4396	GCA_014649775.1	28044	28044	type	True	90.6471	2432	3287	95	below_threshold
Streptomyces alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	86.0517	1576	3287	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	86.0201	2188	3287	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	86.0015	1827	3287	95	below_threshold
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	85.9542	1902	3287	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	85.9431	1889	3287	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004127445.1	1642299	1642299	type	True	85.2976	1855	3287	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	85.2967	1794	3287	95	below_threshold
Streptomyces aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	84.5513	2022	3287	95	below_threshold
Streptomyces lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	84.4064	2032	3287	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	84.3076	2029	3287	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	83.9647	1992	3287	95	below_threshold
Streptomyces albidochromogenes	strain=DSM 41800	GCA_005981925.1	329524	329524	type	True	82.5443	1262	3287	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	82.4898	1483	3287	95	below_threshold
Streptomyces violascens	strain=NBRC 12920	GCA_020521295.1	67381	67381	type	True	82.1631	1568	3287	95	below_threshold
Streptomyces violascens	strain=JCM 4424	GCA_014649955.1	67381	67381	type	True	82.0701	1544	3287	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	82.0149	1780	3287	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	81.7997	1568	3287	95	below_threshold
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	79.5693	1095	3287	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:10,852] [INFO] DFAST Taxonomy check result was written to GCF_023498005.1_ASM2349800v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:10,853] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:10,853] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:10,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe5e052d-59f4-4d77-bd26-304aaf282d68/dqc_reference/checkm_data
[2024-01-25 19:57:10,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:10,941] [INFO] Task started: CheckM
[2024-01-25 19:57:10,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023498005.1_ASM2349800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023498005.1_ASM2349800v1_genomic.fna/checkm_input GCF_023498005.1_ASM2349800v1_genomic.fna/checkm_result
[2024-01-25 20:00:15,361] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:15,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.29%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:15,388] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:15,388] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:15,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023498005.1_ASM2349800v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:15,389] [INFO] Task started: Blastn
[2024-01-25 20:00:15,389] [INFO] Running command: blastn -query GCF_023498005.1_ASM2349800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe5e052d-59f4-4d77-bd26-304aaf282d68/dqc_reference/reference_markers_gtdb.fasta -out GCF_023498005.1_ASM2349800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:17,678] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:17,681] [INFO] Selected 16 target genomes.
[2024-01-25 20:00:17,681] [INFO] Target genome list was writen to GCF_023498005.1_ASM2349800v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:17,715] [INFO] Task started: fastANI
[2024-01-25 20:00:17,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c982572-c0e3-4f7d-992e-c44ce7fa61ec/GCF_023498005.1_ASM2349800v1_genomic.fna.gz --refList GCF_023498005.1_ASM2349800v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023498005.1_ASM2349800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:56,134] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:56,148] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:00:56,149] [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_009769735.1	s__Streptomyces sp009769735	91.9956	2541	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649775.1	s__Streptomyces longisporoflavus	90.6602	2430	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684775.1	s__Streptomyces sp004684775	89.3148	1980	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003945545.1	s__Streptomyces sp003945545	86.0724	1944	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704495.1	s__Streptomyces kanamyceticus	86.0328	2182	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_002556545.1	s__Streptomyces formicae	86.0067	2174	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704395.1	s__Streptomyces alboniger	85.9482	1899	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.40	96.83	0.93	0.87	3	-
GCF_004127445.1	s__Streptomyces alfalfae	85.2366	1868	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	-
GCF_014649395.1	s__Streptomyces aureoverticillatus	84.5678	2019	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646335.1	s__Streptomyces lasiicapitis	84.4092	2030	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.86	0.95	0.95	2	-
GCF_008905045.1	s__Streptomyces albicerus	82.8007	1862	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045015.1	s__Streptomyces scabichelini	82.5056	1672	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003719395.1	s__Streptomyces altiplanensis	82.4093	1399	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	96.26	0.83	0.83	2	-
GCF_018614055.1	s__Streptomyces sp018614055	82.2001	1491	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646115.1	s__Streptomyces camponoticapitis	81.0614	1399	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203645.1	s__Streptomyces zagrosensis	79.5813	1093	3287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:56,150] [INFO] GTDB search result was written to GCF_023498005.1_ASM2349800v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:56,151] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:56,154] [INFO] DFAST_QC result json was written to GCF_023498005.1_ASM2349800v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:56,154] [INFO] DFAST_QC completed!
[2024-01-25 20:00:56,154] [INFO] Total running time: 0h5m5s