[2024-01-24 12:06:34,884] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:34,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:34,888] [INFO] DQC Reference Directory: /var/lib/cwl/stg43a813ed-c387-4c7d-94ed-24f46663ea6c/dqc_reference
[2024-01-24 12:06:36,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:36,178] [INFO] Task started: Prodigal
[2024-01-24 12:06:36,178] [INFO] Running command: gunzip -c /var/lib/cwl/stg24e81220-615f-4745-ba6d-bf60fdae398d/GCF_002154495.1_ASM215449v1_genomic.fna.gz | prodigal -d GCF_002154495.1_ASM215449v1_genomic.fna/cds.fna -a GCF_002154495.1_ASM215449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:58,366] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:58,366] [INFO] Task started: HMMsearch
[2024-01-24 12:06:58,367] [INFO] Running command: hmmsearch --tblout GCF_002154495.1_ASM215449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43a813ed-c387-4c7d-94ed-24f46663ea6c/dqc_reference/reference_markers.hmm GCF_002154495.1_ASM215449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:58,718] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:58,720] [INFO] Found 6/6 markers.
[2024-01-24 12:06:58,785] [INFO] Query marker FASTA was written to GCF_002154495.1_ASM215449v1_genomic.fna/markers.fasta
[2024-01-24 12:06:58,786] [INFO] Task started: Blastn
[2024-01-24 12:06:58,786] [INFO] Running command: blastn -query GCF_002154495.1_ASM215449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43a813ed-c387-4c7d-94ed-24f46663ea6c/dqc_reference/reference_markers.fasta -out GCF_002154495.1_ASM215449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:00,033] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:00,038] [INFO] Selected 14 target genomes.
[2024-01-24 12:07:00,038] [INFO] Target genome list was writen to GCF_002154495.1_ASM215449v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:00,044] [INFO] Task started: fastANI
[2024-01-24 12:07:00,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg24e81220-615f-4745-ba6d-bf60fdae398d/GCF_002154495.1_ASM215449v1_genomic.fna.gz --refList GCF_002154495.1_ASM215449v1_genomic.fna/target_genomes.txt --output GCF_002154495.1_ASM215449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:26,175] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:26,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43a813ed-c387-4c7d-94ed-24f46663ea6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:26,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43a813ed-c387-4c7d-94ed-24f46663ea6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:26,190] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:07:26,190] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:26,190] [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 cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	100.0	2225	2259	95	conclusive
Streptomyces cacaoi	strain=NBRC 12748	GCA_006539165.1	1898	1898	type	True	99.915	2189	2259	95	conclusive
Streptomyces cacaoi	strain=DSM 40057	GCA_013004455.1	1898	1898	type	True	99.8425	2068	2259	95	conclusive
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	82.933	1195	2259	95	below_threshold
Streptomyces reniochalinae	strain=LHW50302	GCA_003323735.1	2250578	2250578	type	True	82.7882	1329	2259	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	82.7735	1367	2259	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	82.748	1368	2259	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	82.7141	1218	2259	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	79.5943	1047	2259	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	79.5185	996	2259	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	79.4606	1030	2259	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	79.4047	820	2259	95	below_threshold
Actinacidiphila glaucinigra	strain=CGMCC 4.1858	GCA_900188405.1	235986	235986	type	True	79.1829	1051	2259	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	79.1182	1038	2259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:26,192] [INFO] DFAST Taxonomy check result was written to GCF_002154495.1_ASM215449v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:26,193] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:26,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:26,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43a813ed-c387-4c7d-94ed-24f46663ea6c/dqc_reference/checkm_data
[2024-01-24 12:07:26,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:26,272] [INFO] Task started: CheckM
[2024-01-24 12:07:26,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002154495.1_ASM215449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002154495.1_ASM215449v1_genomic.fna/checkm_input GCF_002154495.1_ASM215449v1_genomic.fna/checkm_result
[2024-01-24 12:09:09,129] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:09,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.54%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:09,162] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:09,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:09,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002154495.1_ASM215449v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:09,163] [INFO] Task started: Blastn
[2024-01-24 12:09:09,163] [INFO] Running command: blastn -query GCF_002154495.1_ASM215449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43a813ed-c387-4c7d-94ed-24f46663ea6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002154495.1_ASM215449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:11,134] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:11,137] [INFO] Selected 14 target genomes.
[2024-01-24 12:09:11,137] [INFO] Target genome list was writen to GCF_002154495.1_ASM215449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:11,146] [INFO] Task started: fastANI
[2024-01-24 12:09:11,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg24e81220-615f-4745-ba6d-bf60fdae398d/GCF_002154495.1_ASM215449v1_genomic.fna.gz --refList GCF_002154495.1_ASM215449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002154495.1_ASM215449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:35,441] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:35,458] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:35,458] [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_006539165.1	s__Streptomyces cacaoi	99.915	2189	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.44	99.09	0.96	0.94	7	conclusive
GCF_013302895.1	s__Streptomyces chlorinus	83.0757	1341	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676345.1	s__Streptomyces smyrnaeus	82.9311	1307	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.11	97.08	0.90	0.88	5	-
GCF_017676365.1	s__Streptomyces oryzae	82.8978	1200	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323715.1	s__Streptomyces diacarni	82.8839	1319	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323735.1	s__Streptomyces reniochalinae	82.819	1325	2259	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	82.7739	1368	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	97.77	0.97	0.92	14	-
GCF_017676385.1	s__Streptomyces sp017676385	82.7353	1213	2259	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	82.7287	1330	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424765.1	s__Streptomyces sp000424765	82.6195	1258	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.13	98.98	0.93	0.92	5	-
GCF_900111245.1	s__Streptomyces qinglanensis	82.5986	1234	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000424825.1	s__Streptomyces sp000424825	80.4441	1025	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553455.1	s__Streptomyces hygroscopicus	80.0864	1024	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
GCF_900188405.1	s__Streptomyces glauciniger	79.1712	1052	2259	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.86	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:35,460] [INFO] GTDB search result was written to GCF_002154495.1_ASM215449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:35,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:35,466] [INFO] DFAST_QC result json was written to GCF_002154495.1_ASM215449v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:35,466] [INFO] DFAST_QC completed!
[2024-01-24 12:09:35,466] [INFO] Total running time: 0h3m1s