[2024-01-25 17:35:35,525] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:35,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:35,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg487645e6-90aa-4b4d-b34f-5d32aebe1a38/dqc_reference
[2024-01-25 17:35:36,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:36,659] [INFO] Task started: Prodigal
[2024-01-25 17:35:36,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg76e27867-59a2-4375-81ce-35ebd25b9df2/GCF_003323715.1_ASM332371v1_genomic.fna.gz | prodigal -d GCF_003323715.1_ASM332371v1_genomic.fna/cds.fna -a GCF_003323715.1_ASM332371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:56,715] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:56,715] [INFO] Task started: HMMsearch
[2024-01-25 17:35:56,715] [INFO] Running command: hmmsearch --tblout GCF_003323715.1_ASM332371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg487645e6-90aa-4b4d-b34f-5d32aebe1a38/dqc_reference/reference_markers.hmm GCF_003323715.1_ASM332371v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:57,027] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:57,028] [INFO] Found 6/6 markers.
[2024-01-25 17:35:57,087] [INFO] Query marker FASTA was written to GCF_003323715.1_ASM332371v1_genomic.fna/markers.fasta
[2024-01-25 17:35:57,087] [INFO] Task started: Blastn
[2024-01-25 17:35:57,087] [INFO] Running command: blastn -query GCF_003323715.1_ASM332371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg487645e6-90aa-4b4d-b34f-5d32aebe1a38/dqc_reference/reference_markers.fasta -out GCF_003323715.1_ASM332371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:58,412] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:58,415] [INFO] Selected 16 target genomes.
[2024-01-25 17:35:58,415] [INFO] Target genome list was writen to GCF_003323715.1_ASM332371v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:58,420] [INFO] Task started: fastANI
[2024-01-25 17:35:58,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg76e27867-59a2-4375-81ce-35ebd25b9df2/GCF_003323715.1_ASM332371v1_genomic.fna.gz --refList GCF_003323715.1_ASM332371v1_genomic.fna/target_genomes.txt --output GCF_003323715.1_ASM332371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:28,969] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:28,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg487645e6-90aa-4b4d-b34f-5d32aebe1a38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:28,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg487645e6-90aa-4b4d-b34f-5d32aebe1a38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:28,981] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:36:28,981] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:28,981] [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 diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	100.0	2520	2524	95	conclusive
Streptomyces reniochalinae	strain=LHW50302	GCA_003323735.1	2250578	2250578	type	True	94.2627	2148	2524	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	85.4808	1696	2524	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	85.4559	1704	2524	95	below_threshold
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	85.1131	1741	2524	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	85.1101	1487	2524	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	84.9507	1610	2524	95	below_threshold
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	84.804	1593	2524	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	84.7519	1598	2524	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	82.8839	1316	2524	95	below_threshold
Streptomyces cacaoi	strain=NBRC 12748	GCA_006539165.1	1898	1898	type	True	82.76	1555	2524	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.1836	1205	2524	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.1285	1224	2524	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	80.1263	854	2524	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.1082	1188	2524	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.6784	1244	2524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:28,983] [INFO] DFAST Taxonomy check result was written to GCF_003323715.1_ASM332371v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:28,984] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:28,984] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:28,984] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg487645e6-90aa-4b4d-b34f-5d32aebe1a38/dqc_reference/checkm_data
[2024-01-25 17:36:28,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:29,056] [INFO] Task started: CheckM
[2024-01-25 17:36:29,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003323715.1_ASM332371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003323715.1_ASM332371v1_genomic.fna/checkm_input GCF_003323715.1_ASM332371v1_genomic.fna/checkm_result
[2024-01-25 17:38:24,887] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:24,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:24,920] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:24,920] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:24,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003323715.1_ASM332371v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:24,922] [INFO] Task started: Blastn
[2024-01-25 17:38:24,922] [INFO] Running command: blastn -query GCF_003323715.1_ASM332371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg487645e6-90aa-4b4d-b34f-5d32aebe1a38/dqc_reference/reference_markers_gtdb.fasta -out GCF_003323715.1_ASM332371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:27,111] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:27,114] [INFO] Selected 8 target genomes.
[2024-01-25 17:38:27,114] [INFO] Target genome list was writen to GCF_003323715.1_ASM332371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:27,118] [INFO] Task started: fastANI
[2024-01-25 17:38:27,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg76e27867-59a2-4375-81ce-35ebd25b9df2/GCF_003323715.1_ASM332371v1_genomic.fna.gz --refList GCF_003323715.1_ASM332371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003323715.1_ASM332371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:43,343] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:43,349] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:43,350] [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_003323715.1	s__Streptomyces diacarni	100.0	2520	2524	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_003323735.1	s__Streptomyces reniochalinae	94.2365	2151	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424785.1	s__Streptomyces sp000424785	87.0247	1883	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302895.1	s__Streptomyces chlorinus	86.2658	1734	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725885.1	s__Streptomyces albus	85.4458	1705	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	97.77	0.97	0.92	14	-
GCF_017676345.1	s__Streptomyces smyrnaeus	85.1097	1743	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.11	97.08	0.90	0.88	5	-
GCF_900111245.1	s__Streptomyces qinglanensis	84.7975	1594	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_006539165.1	s__Streptomyces cacaoi	82.7941	1547	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.44	99.09	0.96	0.94	7	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:43,351] [INFO] GTDB search result was written to GCF_003323715.1_ASM332371v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:43,352] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:43,356] [INFO] DFAST_QC result json was written to GCF_003323715.1_ASM332371v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:43,356] [INFO] DFAST_QC completed!
[2024-01-25 17:38:43,356] [INFO] Total running time: 0h3m8s