[2023-06-19 02:10:59,551] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:10:59,554] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:10:59,554] [INFO] DQC Reference Directory: /var/lib/cwl/stgada2e568-573c-4a3e-a489-70ce4b747065/dqc_reference
[2023-06-19 02:11:00,819] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:11:00,821] [INFO] Task started: Prodigal
[2023-06-19 02:11:00,821] [INFO] Running command: gunzip -c /var/lib/cwl/stg53eb43d7-6e03-4948-9a81-4ca7775ee237/GCA_018970745.1_ASM1897074v1_genomic.fna.gz | prodigal -d GCA_018970745.1_ASM1897074v1_genomic.fna/cds.fna -a GCA_018970745.1_ASM1897074v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:11:08,089] [INFO] Task succeeded: Prodigal
[2023-06-19 02:11:08,089] [INFO] Task started: HMMsearch
[2023-06-19 02:11:08,089] [INFO] Running command: hmmsearch --tblout GCA_018970745.1_ASM1897074v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgada2e568-573c-4a3e-a489-70ce4b747065/dqc_reference/reference_markers.hmm GCA_018970745.1_ASM1897074v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:11:08,331] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:11:08,333] [INFO] Found 6/6 markers.
[2023-06-19 02:11:08,367] [INFO] Query marker FASTA was written to GCA_018970745.1_ASM1897074v1_genomic.fna/markers.fasta
[2023-06-19 02:11:08,368] [INFO] Task started: Blastn
[2023-06-19 02:11:08,368] [INFO] Running command: blastn -query GCA_018970745.1_ASM1897074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgada2e568-573c-4a3e-a489-70ce4b747065/dqc_reference/reference_markers.fasta -out GCA_018970745.1_ASM1897074v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:11:09,489] [INFO] Task succeeded: Blastn
[2023-06-19 02:11:09,493] [INFO] Selected 34 target genomes.
[2023-06-19 02:11:09,494] [INFO] Target genome list was writen to GCA_018970745.1_ASM1897074v1_genomic.fna/target_genomes.txt
[2023-06-19 02:11:09,501] [INFO] Task started: fastANI
[2023-06-19 02:11:09,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg53eb43d7-6e03-4948-9a81-4ca7775ee237/GCA_018970745.1_ASM1897074v1_genomic.fna.gz --refList GCA_018970745.1_ASM1897074v1_genomic.fna/target_genomes.txt --output GCA_018970745.1_ASM1897074v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:11:39,021] [INFO] Task succeeded: fastANI
[2023-06-19 02:11:39,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgada2e568-573c-4a3e-a489-70ce4b747065/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:11:39,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgada2e568-573c-4a3e-a489-70ce4b747065/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:11:39,049] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:11:39,049] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 02:11:39,049] [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
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	77.3296	175	765	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	77.1652	153	765	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	77.1362	149	765	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	77.0805	113	765	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	77.0593	147	765	95	below_threshold
Motilibacter rhizosphaerae	strain=DSM 45622	GCA_004216915.1	598652	598652	type	True	77.0363	172	765	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	77.0337	141	765	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	77.0188	159	765	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	76.9608	178	765	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	76.9548	147	765	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	76.9087	161	765	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	76.9038	175	765	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	76.8831	135	765	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	76.8446	179	765	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	76.812	155	765	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	76.7753	163	765	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	76.7584	147	765	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	76.7264	163	765	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	76.695	122	765	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	76.6908	167	765	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_000715845.1	371720	371720	type	True	76.6703	150	765	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	76.6474	150	765	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	76.6361	147	765	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	76.6004	170	765	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	76.5861	171	765	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=ATCC 10970	GCA_000331185.2	132474	1927	type	True	76.5791	154	765	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	76.5787	153	765	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	76.5704	172	765	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	76.5591	174	765	95	below_threshold
Microbispora corallina	strain=NBRC 16416	GCA_016863035.1	83302	83302	type	True	76.5362	157	765	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	76.4852	148	765	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	76.3343	166	765	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	76.3244	59	765	95	below_threshold
Actinomadura macra	strain=NBRC 14102	GCA_001552215.1	46164	46164	type	True	76.3004	135	765	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:11:39,052] [INFO] DFAST Taxonomy check result was written to GCA_018970745.1_ASM1897074v1_genomic.fna/tc_result.tsv
[2023-06-19 02:11:39,052] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:11:39,052] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:11:39,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgada2e568-573c-4a3e-a489-70ce4b747065/dqc_reference/checkm_data
[2023-06-19 02:11:39,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:11:39,083] [INFO] Task started: CheckM
[2023-06-19 02:11:39,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018970745.1_ASM1897074v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018970745.1_ASM1897074v1_genomic.fna/checkm_input GCA_018970745.1_ASM1897074v1_genomic.fna/checkm_result
[2023-06-19 02:12:05,981] [INFO] Task succeeded: CheckM
[2023-06-19 02:12:05,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:12:06,013] [INFO] ===== Completeness check finished =====
[2023-06-19 02:12:06,014] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:12:06,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018970745.1_ASM1897074v1_genomic.fna/markers.fasta)
[2023-06-19 02:12:06,015] [INFO] Task started: Blastn
[2023-06-19 02:12:06,015] [INFO] Running command: blastn -query GCA_018970745.1_ASM1897074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgada2e568-573c-4a3e-a489-70ce4b747065/dqc_reference/reference_markers_gtdb.fasta -out GCA_018970745.1_ASM1897074v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:12:07,637] [INFO] Task succeeded: Blastn
[2023-06-19 02:12:07,643] [INFO] Selected 13 target genomes.
[2023-06-19 02:12:07,643] [INFO] Target genome list was writen to GCA_018970745.1_ASM1897074v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:12:07,764] [INFO] Task started: fastANI
[2023-06-19 02:12:07,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg53eb43d7-6e03-4948-9a81-4ca7775ee237/GCA_018970745.1_ASM1897074v1_genomic.fna.gz --refList GCA_018970745.1_ASM1897074v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018970745.1_ASM1897074v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:12:17,270] [INFO] Task succeeded: fastANI
[2023-06-19 02:12:17,285] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:12:17,286] [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_903848435.1	s__Mxb001 sp903848435	95.5521	401	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	96.93	95.89	0.80	0.74	3	conclusive
GCA_004379115.1	s__Mxb001 sp004379115	84.4404	513	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870515.1	s__Mxb001 sp016870515	81.6121	505	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870425.1	s__Mxb001 sp016870425	80.1443	359	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903909555.1	s__Mxb001 sp903909555	79.5451	360	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	99.15	99.05	0.83	0.81	4	-
GCA_903954205.1	s__Mxb001 sp903954205	79.3066	283	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	98.46	98.20	0.79	0.70	14	-
GCA_018970025.1	s__REEB460 sp018970025	77.6453	192	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__REEB460	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125355.1	s__UBA10649 sp016125355	77.5974	231	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025965.2	s__Phycicoccus flavus	76.9441	150	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650495.1	s__Streptomyces cinnamoneus	76.7551	174	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655595.1	s__Streptomyces griseocarneus	76.728	164	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008634025.1	s__Streptomyces albofaciens	76.7195	145	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704655.1	s__Streptomyces rimosus	76.5924	150	765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	96.53	0.95	0.89	49	-
--------------------------------------------------------------------------------
[2023-06-19 02:12:17,288] [INFO] GTDB search result was written to GCA_018970745.1_ASM1897074v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:12:17,288] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:12:17,293] [INFO] DFAST_QC result json was written to GCA_018970745.1_ASM1897074v1_genomic.fna/dqc_result.json
[2023-06-19 02:12:17,293] [INFO] DFAST_QC completed!
[2023-06-19 02:12:17,293] [INFO] Total running time: 0h1m18s