[2023-06-17 15:47:10,935] [INFO] DFAST_QC pipeline started.
[2023-06-17 15:47:10,948] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 15:47:10,948] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ce63f01-5919-443d-a436-321f0b57f3f1/dqc_reference
[2023-06-17 15:47:12,986] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 15:47:12,986] [INFO] Task started: Prodigal
[2023-06-17 15:47:12,987] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0e4294c-9a24-4f7d-9b14-a21fb998fad3/GCA_003556145.1_ASM355614v1_genomic.fna.gz | prodigal -d GCA_003556145.1_ASM355614v1_genomic.fna/cds.fna -a GCA_003556145.1_ASM355614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 15:47:20,311] [INFO] Task succeeded: Prodigal
[2023-06-17 15:47:20,312] [INFO] Task started: HMMsearch
[2023-06-17 15:47:20,312] [INFO] Running command: hmmsearch --tblout GCA_003556145.1_ASM355614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ce63f01-5919-443d-a436-321f0b57f3f1/dqc_reference/reference_markers.hmm GCA_003556145.1_ASM355614v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 15:47:20,532] [INFO] Task succeeded: HMMsearch
[2023-06-17 15:47:20,533] [INFO] Found 6/6 markers.
[2023-06-17 15:47:20,568] [INFO] Query marker FASTA was written to GCA_003556145.1_ASM355614v1_genomic.fna/markers.fasta
[2023-06-17 15:47:20,569] [INFO] Task started: Blastn
[2023-06-17 15:47:20,569] [INFO] Running command: blastn -query GCA_003556145.1_ASM355614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ce63f01-5919-443d-a436-321f0b57f3f1/dqc_reference/reference_markers.fasta -out GCA_003556145.1_ASM355614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:47:21,429] [INFO] Task succeeded: Blastn
[2023-06-17 15:47:21,434] [INFO] Selected 19 target genomes.
[2023-06-17 15:47:21,434] [INFO] Target genome list was writen to GCA_003556145.1_ASM355614v1_genomic.fna/target_genomes.txt
[2023-06-17 15:47:21,444] [INFO] Task started: fastANI
[2023-06-17 15:47:21,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0e4294c-9a24-4f7d-9b14-a21fb998fad3/GCA_003556145.1_ASM355614v1_genomic.fna.gz --refList GCA_003556145.1_ASM355614v1_genomic.fna/target_genomes.txt --output GCA_003556145.1_ASM355614v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 15:47:39,164] [INFO] Task succeeded: fastANI
[2023-06-17 15:47:39,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ce63f01-5919-443d-a436-321f0b57f3f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 15:47:39,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ce63f01-5919-443d-a436-321f0b57f3f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 15:47:39,179] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 15:47:39,179] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 15:47:39,180] [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
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	78.2817	286	776	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	78.2788	287	776	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	77.8983	303	776	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	76.7361	167	776	95	below_threshold
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	75.93	118	776	95	below_threshold
Euzebya rosea	strain=DSW09	GCA_003073135.1	2052804	2052804	type	True	75.7932	121	776	95	below_threshold
Egibacter rhizosphaerae	strain=EGI 80759	GCA_004322855.1	1670831	1670831	type	True	75.7456	105	776	95	below_threshold
Nonomuraea longispora	strain=KC201	GCA_004348345.1	1848320	1848320	type	True	75.5595	108	776	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	75.539	98	776	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	75.4112	76	776	95	below_threshold
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	75.3895	120	776	95	below_threshold
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	75.3767	74	776	95	below_threshold
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	75.3707	122	776	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	75.3301	78	776	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	75.2724	67	776	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	75.2614	111	776	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	75.2524	122	776	95	below_threshold
Kibdelosporangium banguiense	strain=DSM 46670	GCA_017876405.1	1365924	1365924	type	True	75.2075	91	776	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	75.1466	83	776	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 15:47:39,182] [INFO] DFAST Taxonomy check result was written to GCA_003556145.1_ASM355614v1_genomic.fna/tc_result.tsv
[2023-06-17 15:47:39,182] [INFO] ===== Taxonomy check completed =====
[2023-06-17 15:47:39,183] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 15:47:39,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ce63f01-5919-443d-a436-321f0b57f3f1/dqc_reference/checkm_data
[2023-06-17 15:47:39,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 15:47:39,219] [INFO] Task started: CheckM
[2023-06-17 15:47:39,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003556145.1_ASM355614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003556145.1_ASM355614v1_genomic.fna/checkm_input GCA_003556145.1_ASM355614v1_genomic.fna/checkm_result
[2023-06-17 15:48:19,186] [INFO] Task succeeded: CheckM
[2023-06-17 15:48:19,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.91%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 15:48:19,212] [INFO] ===== Completeness check finished =====
[2023-06-17 15:48:19,212] [INFO] ===== Start GTDB Search =====
[2023-06-17 15:48:19,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003556145.1_ASM355614v1_genomic.fna/markers.fasta)
[2023-06-17 15:48:19,213] [INFO] Task started: Blastn
[2023-06-17 15:48:19,213] [INFO] Running command: blastn -query GCA_003556145.1_ASM355614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ce63f01-5919-443d-a436-321f0b57f3f1/dqc_reference/reference_markers_gtdb.fasta -out GCA_003556145.1_ASM355614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:48:20,381] [INFO] Task succeeded: Blastn
[2023-06-17 15:48:20,386] [INFO] Selected 17 target genomes.
[2023-06-17 15:48:20,386] [INFO] Target genome list was writen to GCA_003556145.1_ASM355614v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 15:48:20,395] [INFO] Task started: fastANI
[2023-06-17 15:48:20,395] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0e4294c-9a24-4f7d-9b14-a21fb998fad3/GCA_003556145.1_ASM355614v1_genomic.fna.gz --refList GCA_003556145.1_ASM355614v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003556145.1_ASM355614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 15:48:30,362] [INFO] Task succeeded: fastANI
[2023-06-17 15:48:30,378] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 15:48:30,378] [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
GCA_007136095.1	s__CSSed11-175R1 sp007136095	99.5101	662	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__CSSed11-175R1	95.0	99.27	97.70	0.87	0.80	7	conclusive
GCA_003563915.1	s__CSSed11-175R1 sp003563915	79.4268	359	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__CSSed11-175R1	95.0	99.36	99.32	0.88	0.87	4	-
GCA_007120465.1	s__CSSed11-175R1 sp007120465	79.135	295	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__CSSed11-175R1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003558435.1	s__PWLR01 sp003558435	78.8468	334	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__PWLR01	95.0	99.63	99.63	0.94	0.94	2	-
GCA_007133465.1	s__SLMP01 sp007133465	78.5943	248	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SLMP01	95.0	99.22	99.05	0.81	0.81	3	-
GCA_003554005.1	s__T1Sed10-7 sp003554005	78.2953	214	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	98.88	98.67	0.78	0.76	5	-
GCF_004300825.1	s__Egicoccus halophilus	78.2862	287	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Egicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007120485.1	s__SKTG01 sp007120485	78.2355	212	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKTG01	95.0	98.43	98.43	0.68	0.68	2	-
GCA_007121785.1	s__SKTG01 sp007121785	78.2257	269	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKTG01	95.0	99.65	99.65	0.87	0.87	2	-
GCA_003561535.1	s__T1Sed10-7 sp003561535	78.0857	244	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	98.89	95.80	0.87	0.76	8	-
GCA_018335555.1	s__Egicoccus sp018335555	77.9994	210	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Egicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969705.1	s__Nitriliruptor alkaliphilus	77.8866	304	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Nitriliruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120565.1	s__CSSed11-175R1 sp007120565	77.785	193	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__CSSed11-175R1	95.0	98.07	98.07	0.71	0.71	2	-
GCA_007122985.1	s__SKTG01 sp007122985	77.674	221	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007130695.1	s__SKLC01 sp007130695	77.6068	236	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKLC01	95.0	99.35	99.35	0.92	0.92	2	-
GCA_007125475.1	s__SLDB01 sp007125475	77.3244	193	776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SLDB01	95.0	98.81	98.81	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-06-17 15:48:30,380] [INFO] GTDB search result was written to GCA_003556145.1_ASM355614v1_genomic.fna/result_gtdb.tsv
[2023-06-17 15:48:30,381] [INFO] ===== GTDB Search completed =====
[2023-06-17 15:48:30,385] [INFO] DFAST_QC result json was written to GCA_003556145.1_ASM355614v1_genomic.fna/dqc_result.json
[2023-06-17 15:48:30,385] [INFO] DFAST_QC completed!
[2023-06-17 15:48:30,385] [INFO] Total running time: 0h1m19s