[2024-01-25 18:09:50,691] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:50,693] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:50,693] [INFO] DQC Reference Directory: /var/lib/cwl/stg60c80ddb-b92a-4279-b8c8-18ecba71e1e0/dqc_reference
[2024-01-25 18:09:51,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:51,864] [INFO] Task started: Prodigal
[2024-01-25 18:09:51,864] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe518aa0-4553-4f9b-9410-07c4dfcd97c2/GCF_000720475.1_ASM72047v1_genomic.fna.gz | prodigal -d GCF_000720475.1_ASM72047v1_genomic.fna/cds.fna -a GCF_000720475.1_ASM72047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:15,214] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:15,214] [INFO] Task started: HMMsearch
[2024-01-25 18:10:15,214] [INFO] Running command: hmmsearch --tblout GCF_000720475.1_ASM72047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60c80ddb-b92a-4279-b8c8-18ecba71e1e0/dqc_reference/reference_markers.hmm GCF_000720475.1_ASM72047v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:15,559] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:15,560] [INFO] Found 6/6 markers.
[2024-01-25 18:10:15,626] [INFO] Query marker FASTA was written to GCF_000720475.1_ASM72047v1_genomic.fna/markers.fasta
[2024-01-25 18:10:15,626] [INFO] Task started: Blastn
[2024-01-25 18:10:15,626] [INFO] Running command: blastn -query GCF_000720475.1_ASM72047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60c80ddb-b92a-4279-b8c8-18ecba71e1e0/dqc_reference/reference_markers.fasta -out GCF_000720475.1_ASM72047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:16,824] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:16,827] [INFO] Selected 20 target genomes.
[2024-01-25 18:10:16,828] [INFO] Target genome list was writen to GCF_000720475.1_ASM72047v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:16,846] [INFO] Task started: fastANI
[2024-01-25 18:10:16,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe518aa0-4553-4f9b-9410-07c4dfcd97c2/GCF_000720475.1_ASM72047v1_genomic.fna.gz --refList GCF_000720475.1_ASM72047v1_genomic.fna/target_genomes.txt --output GCF_000720475.1_ASM72047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:02,315] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:02,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60c80ddb-b92a-4279-b8c8-18ecba71e1e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:02,315] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60c80ddb-b92a-4279-b8c8-18ecba71e1e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:02,327] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:11:02,327] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:11:02,328] [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 aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	88.6346	2161	3027	95	below_threshold
Streptomyces lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	88.2143	2149	3027	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	88.1377	2144	3027	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_014650815.1	68200	68200	type	True	88.1322	2128	3027	95	below_threshold
Streptomyces alboflavus	strain=NRRL B-2373	GCA_000716675.1	67267	67267	type	True	88.0924	2149	3027	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	86.0696	2045	3027	95	below_threshold
Streptomyces longispororuber	strain=JCM 4784	GCA_014656095.1	68230	68230	type	True	85.7527	1929	3027	95	below_threshold
Streptomyces alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	84.4111	1504	3027	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	84.344	1612	3027	95	below_threshold
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	84.2521	1775	3027	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	84.0556	1659	3027	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	83.8871	1812	3027	95	below_threshold
Streptomyces longisporoflavus	strain=JCM 4396	GCA_014649775.1	28044	28044	type	True	83.6442	1790	3027	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	82.1469	1512	3027	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	81.9116	1482	3027	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	81.8408	1328	3027	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	81.7251	1528	3027	95	below_threshold
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	81.7	1389	3027	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	81.6683	1506	3027	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	81.6092	1519	3027	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:02,329] [INFO] DFAST Taxonomy check result was written to GCF_000720475.1_ASM72047v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:02,330] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:02,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:02,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60c80ddb-b92a-4279-b8c8-18ecba71e1e0/dqc_reference/checkm_data
[2024-01-25 18:11:02,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:02,416] [INFO] Task started: CheckM
[2024-01-25 18:11:02,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000720475.1_ASM72047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000720475.1_ASM72047v1_genomic.fna/checkm_input GCF_000720475.1_ASM72047v1_genomic.fna/checkm_result
[2024-01-25 18:12:40,639] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:40,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:40,663] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:40,664] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:40,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000720475.1_ASM72047v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:40,665] [INFO] Task started: Blastn
[2024-01-25 18:12:40,665] [INFO] Running command: blastn -query GCF_000720475.1_ASM72047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60c80ddb-b92a-4279-b8c8-18ecba71e1e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000720475.1_ASM72047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:42,675] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:42,678] [INFO] Selected 13 target genomes.
[2024-01-25 18:12:42,678] [INFO] Target genome list was writen to GCF_000720475.1_ASM72047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:42,694] [INFO] Task started: fastANI
[2024-01-25 18:12:42,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe518aa0-4553-4f9b-9410-07c4dfcd97c2/GCF_000720475.1_ASM72047v1_genomic.fna.gz --refList GCF_000720475.1_ASM72047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000720475.1_ASM72047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:14,278] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:14,287] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:14,288] [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_000720475.1	s__Streptomyces aureocirculatus	100.0	3024	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_009755605.1	s__Streptomyces typhae	92.0681	2383	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.66	98.66	0.93	0.93	2	-
GCF_014649395.1	s__Streptomyces aureoverticillatus	88.6327	2161	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000414115.1	s__Streptomyces aurantiacus_A	88.53	1907	3027	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	88.2242	2148	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.86	0.95	0.95	2	-
GCF_014650815.1	s__Streptomyces flavofungini	88.141	2126	3027	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	88.0734	2153	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.12	98.24	0.94	0.89	5	-
GCF_014656095.1	s__Streptomyces longispororuber	85.7192	1935	3027	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	84.2966	1774	3027	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	83.6402	1790	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	82.0238	1494	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001906585.1	s__Streptomyces kebangsaanensis	81.8727	1321	3027	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	81.7157	1532	3027	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 18:13:14,289] [INFO] GTDB search result was written to GCF_000720475.1_ASM72047v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:14,290] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:14,294] [INFO] DFAST_QC result json was written to GCF_000720475.1_ASM72047v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:14,294] [INFO] DFAST_QC completed!
[2024-01-25 18:13:14,294] [INFO] Total running time: 0h3m24s