[2023-06-29 06:10:54,250] [INFO] DFAST_QC pipeline started.
[2023-06-29 06:10:54,271] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 06:10:54,271] [INFO] DQC Reference Directory: /var/lib/cwl/stgd01c6d76-5df6-4cd4-9741-9722fe3809e8/dqc_reference
[2023-06-29 06:10:57,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 06:10:57,653] [INFO] Task started: Prodigal
[2023-06-29 06:10:57,654] [INFO] Running command: gunzip -c /var/lib/cwl/stgf832742c-837a-4353-a146-fa05dfe071c6/GCA_020724705.1_ASM2072470v1_genomic.fna.gz | prodigal -d GCA_020724705.1_ASM2072470v1_genomic.fna/cds.fna -a GCA_020724705.1_ASM2072470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 06:11:12,608] [INFO] Task succeeded: Prodigal
[2023-06-29 06:11:12,608] [INFO] Task started: HMMsearch
[2023-06-29 06:11:12,608] [INFO] Running command: hmmsearch --tblout GCA_020724705.1_ASM2072470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd01c6d76-5df6-4cd4-9741-9722fe3809e8/dqc_reference/reference_markers.hmm GCA_020724705.1_ASM2072470v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 06:11:12,939] [INFO] Task succeeded: HMMsearch
[2023-06-29 06:11:12,940] [INFO] Found 6/6 markers.
[2023-06-29 06:11:12,987] [INFO] Query marker FASTA was written to GCA_020724705.1_ASM2072470v1_genomic.fna/markers.fasta
[2023-06-29 06:11:12,988] [INFO] Task started: Blastn
[2023-06-29 06:11:12,988] [INFO] Running command: blastn -query GCA_020724705.1_ASM2072470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd01c6d76-5df6-4cd4-9741-9722fe3809e8/dqc_reference/reference_markers.fasta -out GCA_020724705.1_ASM2072470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:11:15,734] [INFO] Task succeeded: Blastn
[2023-06-29 06:11:15,739] [INFO] Selected 31 target genomes.
[2023-06-29 06:11:15,740] [INFO] Target genome list was writen to GCA_020724705.1_ASM2072470v1_genomic.fna/target_genomes.txt
[2023-06-29 06:11:15,812] [INFO] Task started: fastANI
[2023-06-29 06:11:15,812] [INFO] Running command: fastANI --query /var/lib/cwl/stgf832742c-837a-4353-a146-fa05dfe071c6/GCA_020724705.1_ASM2072470v1_genomic.fna.gz --refList GCA_020724705.1_ASM2072470v1_genomic.fna/target_genomes.txt --output GCA_020724705.1_ASM2072470v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 06:11:39,988] [INFO] Task succeeded: fastANI
[2023-06-29 06:11:39,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd01c6d76-5df6-4cd4-9741-9722fe3809e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 06:11:39,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd01c6d76-5df6-4cd4-9741-9722fe3809e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 06:11:40,010] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 06:11:40,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 06:11:40,010] [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
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.4346	112	1627	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	75.382	81	1627	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.3506	135	1627	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.341	104	1627	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	75.326	85	1627	95	below_threshold
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	75.3006	87	1627	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.2703	240	1627	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	75.1778	91	1627	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	75.1359	113	1627	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	75.1327	110	1627	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	75.1317	114	1627	95	below_threshold
Arenimonas fontis	strain=3729k	GCA_008386465.1	2608255	2608255	type	True	75.1039	71	1627	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	75.0936	50	1627	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	75.0618	251	1627	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	75.0426	128	1627	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	75.0054	87	1627	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	75.0051	88	1627	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.0033	197	1627	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	74.9876	91	1627	95	below_threshold
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	74.9439	89	1627	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.94	315	1627	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.9392	325	1627	95	below_threshold
Gordonia lacunae	strain=BS2	GCA_002149015.1	417102	417102	type	True	74.8176	70	1627	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	74.817	99	1627	95	below_threshold
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	74.7785	107	1627	95	below_threshold
Rhodococcus yananensis	strain=FBM22-1	GCA_020515525.1	2879464	2879464	type	True	74.7228	54	1627	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	74.7209	64	1627	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 06:11:40,012] [INFO] DFAST Taxonomy check result was written to GCA_020724705.1_ASM2072470v1_genomic.fna/tc_result.tsv
[2023-06-29 06:11:40,013] [INFO] ===== Taxonomy check completed =====
[2023-06-29 06:11:40,013] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 06:11:40,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd01c6d76-5df6-4cd4-9741-9722fe3809e8/dqc_reference/checkm_data
[2023-06-29 06:11:40,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 06:11:40,068] [INFO] Task started: CheckM
[2023-06-29 06:11:40,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020724705.1_ASM2072470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020724705.1_ASM2072470v1_genomic.fna/checkm_input GCA_020724705.1_ASM2072470v1_genomic.fna/checkm_result
[2023-06-29 06:12:30,210] [INFO] Task succeeded: CheckM
[2023-06-29 06:12:30,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 06:12:30,235] [INFO] ===== Completeness check finished =====
[2023-06-29 06:12:30,236] [INFO] ===== Start GTDB Search =====
[2023-06-29 06:12:30,236] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020724705.1_ASM2072470v1_genomic.fna/markers.fasta)
[2023-06-29 06:12:30,237] [INFO] Task started: Blastn
[2023-06-29 06:12:30,237] [INFO] Running command: blastn -query GCA_020724705.1_ASM2072470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd01c6d76-5df6-4cd4-9741-9722fe3809e8/dqc_reference/reference_markers_gtdb.fasta -out GCA_020724705.1_ASM2072470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:12:31,386] [INFO] Task succeeded: Blastn
[2023-06-29 06:12:31,391] [INFO] Selected 21 target genomes.
[2023-06-29 06:12:31,392] [INFO] Target genome list was writen to GCA_020724705.1_ASM2072470v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 06:12:31,470] [INFO] Task started: fastANI
[2023-06-29 06:12:31,471] [INFO] Running command: fastANI --query /var/lib/cwl/stgf832742c-837a-4353-a146-fa05dfe071c6/GCA_020724705.1_ASM2072470v1_genomic.fna.gz --refList GCA_020724705.1_ASM2072470v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020724705.1_ASM2072470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 06:12:49,377] [INFO] Task succeeded: fastANI
[2023-06-29 06:12:49,397] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 06:12:49,398] [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_002841905.1	s__HGW-17 sp002841905	82.5434	558	1627	d__Bacteria;p__Myxococcota;c__Polyangia;o__HGW-17;f__HGW-17;g__HGW-17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018817795.1	s__HGW-17 sp018817795	82.0842	775	1627	d__Bacteria;p__Myxococcota;c__Polyangia;o__HGW-17;f__HGW-17;g__HGW-17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841825.1	s__HGW-17 sp002841825	82.027	923	1627	d__Bacteria;p__Myxococcota;c__Polyangia;o__HGW-17;f__HGW-17;g__HGW-17	95.0	97.98	97.84	0.81	0.78	4	-
GCA_003249585.1	s__SZUA-580 sp003249585	76.6269	161	1627	d__Bacteria;p__Myxococcota;c__Polyangia;o__HGW-17;f__HGW-17;g__SZUA-580	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	75.3419	135	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012979235.1	s__Dissulfurirhabdus thermomarina	75.3006	87	1627	d__Bacteria;p__Desulfobacterota;c__Dissulfuribacteria;o__Dissulfuribacterales;f__Dissulfurirhabdaceae;g__Dissulfurirhabdus	95.0	99.96	99.96	0.96	0.96	2	-
GCA_016713135.1	s__JADKFD01 sp016713135	75.2242	85	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226565.1	s__PHBI01 sp006226565	75.2235	261	1627	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__PHBI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013085545.1	s__Desulfovibrio_R marinus	75.1978	77	1627	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio_R	95.0	99.02	99.02	0.95	0.95	2	-
GCA_900696455.1	s__UBA2376 sp900696455	75.185	334	1627	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCA_016717005.1	s__UBA2376 sp016717005	75.1604	318	1627	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789885.1	s__SHZI01 sp016789885	75.1513	93	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__SHZI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526095.1	s__WYBA01 sp011526095	75.1503	292	1627	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780435.1	s__SXOO01 sp018780435	75.0679	130	1627	d__Bacteria;p__Myxococcota;c__UBA9042;o__GCA-2863065;f__GCA-2863065;g__SXOO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000069785.1	s__Cupriavidus taiwanensis	75.0054	87	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.86	98.78	0.92	0.91	9	-
GCA_016214985.1	s__JACRMM01 sp016214985	74.976	87	1627	d__Bacteria;p__Desulfobacterota_C;c__Deferrisomatia;o__Deferrisomatales;f__JACRMM01;g__JACRMM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799515.1	s__Phenylobacterium sp004799515	74.9349	118	1627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426385.1	s__Arsenicicoccus bolidensis	74.8129	100	1627	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	98.16	98.06	0.89	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-29 06:12:49,400] [INFO] GTDB search result was written to GCA_020724705.1_ASM2072470v1_genomic.fna/result_gtdb.tsv
[2023-06-29 06:12:49,400] [INFO] ===== GTDB Search completed =====
[2023-06-29 06:12:49,405] [INFO] DFAST_QC result json was written to GCA_020724705.1_ASM2072470v1_genomic.fna/dqc_result.json
[2023-06-29 06:12:49,405] [INFO] DFAST_QC completed!
[2023-06-29 06:12:49,405] [INFO] Total running time: 0h1m55s