[2024-01-24 14:15:29,539] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:29,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:29,541] [INFO] DQC Reference Directory: /var/lib/cwl/stge6c36c58-1bed-47f7-afd2-5884c4268c95/dqc_reference
[2024-01-24 14:15:30,775] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:30,776] [INFO] Task started: Prodigal
[2024-01-24 14:15:30,776] [INFO] Running command: gunzip -c /var/lib/cwl/stga5f72b0c-1b2b-4022-bb4c-5e2c0861ef45/GCF_019400875.1_ASM1940087v1_genomic.fna.gz | prodigal -d GCF_019400875.1_ASM1940087v1_genomic.fna/cds.fna -a GCF_019400875.1_ASM1940087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:48,140] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:48,141] [INFO] Task started: HMMsearch
[2024-01-24 14:15:48,141] [INFO] Running command: hmmsearch --tblout GCF_019400875.1_ASM1940087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6c36c58-1bed-47f7-afd2-5884c4268c95/dqc_reference/reference_markers.hmm GCF_019400875.1_ASM1940087v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:48,411] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:48,412] [INFO] Found 6/6 markers.
[2024-01-24 14:15:48,464] [INFO] Query marker FASTA was written to GCF_019400875.1_ASM1940087v1_genomic.fna/markers.fasta
[2024-01-24 14:15:48,465] [INFO] Task started: Blastn
[2024-01-24 14:15:48,465] [INFO] Running command: blastn -query GCF_019400875.1_ASM1940087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6c36c58-1bed-47f7-afd2-5884c4268c95/dqc_reference/reference_markers.fasta -out GCF_019400875.1_ASM1940087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:49,719] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:49,722] [INFO] Selected 13 target genomes.
[2024-01-24 14:15:49,722] [INFO] Target genome list was writen to GCF_019400875.1_ASM1940087v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:49,730] [INFO] Task started: fastANI
[2024-01-24 14:15:49,730] [INFO] Running command: fastANI --query /var/lib/cwl/stga5f72b0c-1b2b-4022-bb4c-5e2c0861ef45/GCF_019400875.1_ASM1940087v1_genomic.fna.gz --refList GCF_019400875.1_ASM1940087v1_genomic.fna/target_genomes.txt --output GCF_019400875.1_ASM1940087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:13,540] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:13,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6c36c58-1bed-47f7-afd2-5884c4268c95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:13,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6c36c58-1bed-47f7-afd2-5884c4268c95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:13,553] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:16:13,553] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:16:13,553] [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 alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	92.5022	1492	1991	95	below_threshold
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	92.4968	1648	1991	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	88.5208	1418	1991	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	88.3123	1470	1991	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	88.2886	1419	1991	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004127445.1	1642299	1642299	type	True	88.1971	1519	1991	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	87.9035	1536	1991	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	87.8253	1417	1991	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	86.2874	1499	1991	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	84.5669	1488	1991	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	82.9732	1101	1991	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	82.5804	1235	1991	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	82.559	1113	1991	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:13,554] [INFO] DFAST Taxonomy check result was written to GCF_019400875.1_ASM1940087v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:13,555] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:13,555] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:13,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6c36c58-1bed-47f7-afd2-5884c4268c95/dqc_reference/checkm_data
[2024-01-24 14:16:13,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:13,622] [INFO] Task started: CheckM
[2024-01-24 14:16:13,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019400875.1_ASM1940087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019400875.1_ASM1940087v1_genomic.fna/checkm_input GCF_019400875.1_ASM1940087v1_genomic.fna/checkm_result
[2024-01-24 14:17:06,526] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:06,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:06,552] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:06,552] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:06,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019400875.1_ASM1940087v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:06,553] [INFO] Task started: Blastn
[2024-01-24 14:17:06,553] [INFO] Running command: blastn -query GCF_019400875.1_ASM1940087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6c36c58-1bed-47f7-afd2-5884c4268c95/dqc_reference/reference_markers_gtdb.fasta -out GCF_019400875.1_ASM1940087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:08,676] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:08,679] [INFO] Selected 9 target genomes.
[2024-01-24 14:17:08,679] [INFO] Target genome list was writen to GCF_019400875.1_ASM1940087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:08,686] [INFO] Task started: fastANI
[2024-01-24 14:17:08,687] [INFO] Running command: fastANI --query /var/lib/cwl/stga5f72b0c-1b2b-4022-bb4c-5e2c0861ef45/GCF_019400875.1_ASM1940087v1_genomic.fna.gz --refList GCF_019400875.1_ASM1940087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019400875.1_ASM1940087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:25,739] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:25,749] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:25,749] [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_003945545.1	s__Streptomyces sp003945545	95.9884	1836	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008704395.1	s__Streptomyces alboniger	92.509	1647	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.40	96.83	0.93	0.87	3	-
GCA_004010275.1	s__Streptomyces huasconensis	90.2276	1524	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016905445.1	s__Streptomyces sp016905445	90.0821	1510	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419745.1	s__Streptomyces silaceus	88.5555	1415	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.58	0.96	0.96	2	-
GCF_001418325.1	s__Streptomyces atriruber	88.3257	1415	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004127445.1	s__Streptomyces alfalfae	88.2094	1517	1991	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	-
GCF_002556545.1	s__Streptomyces formicae	87.9482	1542	1991	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	86.4235	1306	1991	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 14:17:25,751] [INFO] GTDB search result was written to GCF_019400875.1_ASM1940087v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:25,751] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:25,755] [INFO] DFAST_QC result json was written to GCF_019400875.1_ASM1940087v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:25,755] [INFO] DFAST_QC completed!
[2024-01-24 14:17:25,755] [INFO] Total running time: 0h1m56s