[2024-01-24 14:31:28,716] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:28,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:28,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b6a0927-5ebc-4e0c-8e92-43cdfe1db2e5/dqc_reference
[2024-01-24 14:31:29,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:29,834] [INFO] Task started: Prodigal
[2024-01-24 14:31:29,835] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9c9f3d5-539f-4cba-85e8-7d352a666c44/GCF_005280195.1_ASM528019v1_genomic.fna.gz | prodigal -d GCF_005280195.1_ASM528019v1_genomic.fna/cds.fna -a GCF_005280195.1_ASM528019v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:49,244] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:49,245] [INFO] Task started: HMMsearch
[2024-01-24 14:31:49,245] [INFO] Running command: hmmsearch --tblout GCF_005280195.1_ASM528019v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b6a0927-5ebc-4e0c-8e92-43cdfe1db2e5/dqc_reference/reference_markers.hmm GCF_005280195.1_ASM528019v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:49,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:49,519] [INFO] Found 6/6 markers.
[2024-01-24 14:31:49,574] [INFO] Query marker FASTA was written to GCF_005280195.1_ASM528019v1_genomic.fna/markers.fasta
[2024-01-24 14:31:49,574] [INFO] Task started: Blastn
[2024-01-24 14:31:49,575] [INFO] Running command: blastn -query GCF_005280195.1_ASM528019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b6a0927-5ebc-4e0c-8e92-43cdfe1db2e5/dqc_reference/reference_markers.fasta -out GCF_005280195.1_ASM528019v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:50,812] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:50,814] [INFO] Selected 17 target genomes.
[2024-01-24 14:31:50,815] [INFO] Target genome list was writen to GCF_005280195.1_ASM528019v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:50,824] [INFO] Task started: fastANI
[2024-01-24 14:31:50,824] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9c9f3d5-539f-4cba-85e8-7d352a666c44/GCF_005280195.1_ASM528019v1_genomic.fna.gz --refList GCF_005280195.1_ASM528019v1_genomic.fna/target_genomes.txt --output GCF_005280195.1_ASM528019v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:27,811] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:27,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b6a0927-5ebc-4e0c-8e92-43cdfe1db2e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:27,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b6a0927-5ebc-4e0c-8e92-43cdfe1db2e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:27,822] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:32:27,822] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:32:27,822] [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 galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	100.0	2572	2574	95	conclusive
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	99.996	2545	2574	95	conclusive
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	94.8848	2231	2574	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	85.9941	1810	2574	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.3993	1439	2574	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.3483	1674	2574	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.3148	1694	2574	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.292	1730	2574	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.1457	1441	2574	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	85.0957	1670	2574	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	85.0746	1654	2574	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	85.0663	1666	2574	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.9874	1689	2574	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	84.9482	1674	2574	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	84.8602	1685	2574	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	84.673	1287	2574	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.4113	1701	2574	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:27,823] [INFO] DFAST Taxonomy check result was written to GCF_005280195.1_ASM528019v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:27,824] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:27,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:27,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b6a0927-5ebc-4e0c-8e92-43cdfe1db2e5/dqc_reference/checkm_data
[2024-01-24 14:32:27,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:27,896] [INFO] Task started: CheckM
[2024-01-24 14:32:27,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005280195.1_ASM528019v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005280195.1_ASM528019v1_genomic.fna/checkm_input GCF_005280195.1_ASM528019v1_genomic.fna/checkm_result
[2024-01-24 14:34:14,241] [INFO] Task succeeded: CheckM
[2024-01-24 14:34:14,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:34:14,260] [INFO] ===== Completeness check finished =====
[2024-01-24 14:34:14,260] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:34:14,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005280195.1_ASM528019v1_genomic.fna/markers.fasta)
[2024-01-24 14:34:14,260] [INFO] Task started: Blastn
[2024-01-24 14:34:14,260] [INFO] Running command: blastn -query GCF_005280195.1_ASM528019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b6a0927-5ebc-4e0c-8e92-43cdfe1db2e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_005280195.1_ASM528019v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:34:16,301] [INFO] Task succeeded: Blastn
[2024-01-24 14:34:16,304] [INFO] Selected 19 target genomes.
[2024-01-24 14:34:16,304] [INFO] Target genome list was writen to GCF_005280195.1_ASM528019v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:34:16,314] [INFO] Task started: fastANI
[2024-01-24 14:34:16,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9c9f3d5-539f-4cba-85e8-7d352a666c44/GCF_005280195.1_ASM528019v1_genomic.fna.gz --refList GCF_005280195.1_ASM528019v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005280195.1_ASM528019v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:34:56,670] [INFO] Task succeeded: fastANI
[2024-01-24 14:34:56,681] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:34:56,682] [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_005280195.1	s__Streptomyces galbus	100.0	2572	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	conclusive
GCF_001514125.1	s__Streptomyces longwoodensis	94.8926	2230	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_014656055.1	s__Streptomyces griseosporeus	86.0431	1802	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	85.9399	1780	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019855.1	s__Streptomyces antibioticus_B	85.8393	1753	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.20	96.76	0.94	0.90	5	-
GCF_001514205.1	s__Streptomyces griseoruber	85.735	1770	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363835.1	s__Streptomyces sp004363835	85.6176	1800	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011193355.1	s__Streptomyces sp011193355	85.5268	1702	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761215.1	s__Streptomyces glaucescens	85.3728	1716	2574	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	85.2842	1698	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_019219825.1	s__Streptomyces sp019219825	85.1917	1614	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973465.1	s__Streptomyces sp008973465	85.1798	1670	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	85.0845	1798	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003074055.1	s__Streptomyces nigra	85.0645	1666	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.21	97.15	0.92	0.91	4	-
GCF_006715395.1	s__Streptomyces sp006715395	85.0002	1800	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.35	95.35	0.79	0.79	2	-
GCF_001735805.1	s__Streptomyces fodineus	84.8503	1686	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049285.1	s__Streptomyces sp019049285	84.5969	1669	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857135.1	s__Streptomyces sp009857135	83.9866	1556	2574	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	83.6828	1409	2574	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 14:34:56,683] [INFO] GTDB search result was written to GCF_005280195.1_ASM528019v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:34:56,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:34:56,687] [INFO] DFAST_QC result json was written to GCF_005280195.1_ASM528019v1_genomic.fna/dqc_result.json
[2024-01-24 14:34:56,687] [INFO] DFAST_QC completed!
[2024-01-24 14:34:56,687] [INFO] Total running time: 0h3m28s