[2024-01-25 20:11:35,551] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:11:35,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:11:35,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg69a5650e-fd71-4803-95b7-c4f6b6cf932b/dqc_reference
[2024-01-25 20:11:36,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:11:36,683] [INFO] Task started: Prodigal
[2024-01-25 20:11:36,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg9de561c9-bc7f-4089-bb1a-7491aada4a5a/GCF_011045075.1_ASM1104507v1_genomic.fna.gz | prodigal -d GCF_011045075.1_ASM1104507v1_genomic.fna/cds.fna -a GCF_011045075.1_ASM1104507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:11:54,939] [INFO] Task succeeded: Prodigal
[2024-01-25 20:11:54,940] [INFO] Task started: HMMsearch
[2024-01-25 20:11:54,940] [INFO] Running command: hmmsearch --tblout GCF_011045075.1_ASM1104507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69a5650e-fd71-4803-95b7-c4f6b6cf932b/dqc_reference/reference_markers.hmm GCF_011045075.1_ASM1104507v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:11:55,263] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:11:55,264] [INFO] Found 6/6 markers.
[2024-01-25 20:11:55,326] [INFO] Query marker FASTA was written to GCF_011045075.1_ASM1104507v1_genomic.fna/markers.fasta
[2024-01-25 20:11:55,326] [INFO] Task started: Blastn
[2024-01-25 20:11:55,326] [INFO] Running command: blastn -query GCF_011045075.1_ASM1104507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69a5650e-fd71-4803-95b7-c4f6b6cf932b/dqc_reference/reference_markers.fasta -out GCF_011045075.1_ASM1104507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:11:56,574] [INFO] Task succeeded: Blastn
[2024-01-25 20:11:56,582] [INFO] Selected 19 target genomes.
[2024-01-25 20:11:56,582] [INFO] Target genome list was writen to GCF_011045075.1_ASM1104507v1_genomic.fna/target_genomes.txt
[2024-01-25 20:11:56,609] [INFO] Task started: fastANI
[2024-01-25 20:11:56,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg9de561c9-bc7f-4089-bb1a-7491aada4a5a/GCF_011045075.1_ASM1104507v1_genomic.fna.gz --refList GCF_011045075.1_ASM1104507v1_genomic.fna/target_genomes.txt --output GCF_011045075.1_ASM1104507v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:28,928] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:28,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69a5650e-fd71-4803-95b7-c4f6b6cf932b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:28,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69a5650e-fd71-4803-95b7-c4f6b6cf932b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:28,941] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:28,941] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:28,941] [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 boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	100.0	2184	2210	95	conclusive
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	82.8853	1120	2210	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	82.6387	1182	2210	95	below_threshold
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	82.6065	1254	2210	95	below_threshold
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	82.4338	1160	2210	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	82.418	1178	2210	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	82.2774	1090	2210	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	82.1996	1152	2210	95	below_threshold
Streptomyces reniochalinae	strain=LHW50302	GCA_003323735.1	2250578	2250578	type	True	81.945	1187	2210	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	81.8562	1182	2210	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.3033	1132	2210	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	80.2662	878	2210	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.2093	1093	2210	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.1746	1126	2210	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	79.0837	1019	2210	95	below_threshold
Peterkaempfera bronchialis	strain=DSM 106435	GCA_003258605.2	2126346	2126346	type	True	78.9308	840	2210	95	below_threshold
Streptacidiphilus fuscans	strain=NEAU-YB345	GCA_015690355.1	2789292	2789292	type	True	78.4262	791	2210	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	78.0822	829	2210	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	78.072	837	2210	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:28,942] [INFO] DFAST Taxonomy check result was written to GCF_011045075.1_ASM1104507v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:28,943] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:28,943] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:28,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69a5650e-fd71-4803-95b7-c4f6b6cf932b/dqc_reference/checkm_data
[2024-01-25 20:12:28,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:29,020] [INFO] Task started: CheckM
[2024-01-25 20:12:29,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011045075.1_ASM1104507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011045075.1_ASM1104507v1_genomic.fna/checkm_input GCF_011045075.1_ASM1104507v1_genomic.fna/checkm_result
[2024-01-25 20:13:29,883] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:29,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:29,922] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:29,923] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:29,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011045075.1_ASM1104507v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:29,923] [INFO] Task started: Blastn
[2024-01-25 20:13:29,923] [INFO] Running command: blastn -query GCF_011045075.1_ASM1104507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69a5650e-fd71-4803-95b7-c4f6b6cf932b/dqc_reference/reference_markers_gtdb.fasta -out GCF_011045075.1_ASM1104507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:32,071] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:32,075] [INFO] Selected 15 target genomes.
[2024-01-25 20:13:32,075] [INFO] Target genome list was writen to GCF_011045075.1_ASM1104507v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:32,096] [INFO] Task started: fastANI
[2024-01-25 20:13:32,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg9de561c9-bc7f-4089-bb1a-7491aada4a5a/GCF_011045075.1_ASM1104507v1_genomic.fna.gz --refList GCF_011045075.1_ASM1104507v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011045075.1_ASM1104507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:56,895] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:56,905] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:13:56,905] [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_017676365.1	s__Streptomyces oryzae	82.8485	1125	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676385.1	s__Streptomyces sp017676385	82.6823	1176	2210	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	82.6548	1245	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.11	97.08	0.90	0.88	5	-
GCF_013302895.1	s__Streptomyces chlorinus	82.6056	1198	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111245.1	s__Streptomyces qinglanensis	82.4673	1155	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000424765.1	s__Streptomyces sp000424765	82.3109	1183	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.13	98.98	0.93	0.92	5	-
GCF_000725885.1	s__Streptomyces albus	82.1781	1156	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	97.77	0.97	0.92	14	-
GCF_006539165.1	s__Streptomyces cacaoi	82.1096	1249	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.44	99.09	0.96	0.94	7	-
GCF_000424785.1	s__Streptomyces sp000424785	82.0497	1155	2210	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	81.9537	1186	2210	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	81.8824	1178	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726235.1	s__Streptomyces sp012726235	81.5868	1068	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258605.2	s__Streptomyces_D bronchialis	78.9193	843	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015690355.1	s__Streptacidiphilus fuscans	78.4268	791	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109465.1	s__Streptacidiphilus jiangxiensis	78.0562	832	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:56,906] [INFO] GTDB search result was written to GCF_011045075.1_ASM1104507v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:56,907] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:56,910] [INFO] DFAST_QC result json was written to GCF_011045075.1_ASM1104507v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:56,910] [INFO] DFAST_QC completed!
[2024-01-25 20:13:56,910] [INFO] Total running time: 0h2m21s