[2023-06-29 07:39:31,885] [INFO] DFAST_QC pipeline started.
[2023-06-29 07:39:31,888] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 07:39:31,888] [INFO] DQC Reference Directory: /var/lib/cwl/stgee67c467-5a73-44a6-b1b4-c6218d86ee55/dqc_reference
[2023-06-29 07:39:35,186] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 07:39:35,187] [INFO] Task started: Prodigal
[2023-06-29 07:39:35,187] [INFO] Running command: gunzip -c /var/lib/cwl/stg325e9ea4-2e89-414e-b34d-4a7b177e5968/GCA_020439245.1_ASM2043924v1_genomic.fna.gz | prodigal -d GCA_020439245.1_ASM2043924v1_genomic.fna/cds.fna -a GCA_020439245.1_ASM2043924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 07:39:43,782] [INFO] Task succeeded: Prodigal
[2023-06-29 07:39:43,786] [INFO] Task started: HMMsearch
[2023-06-29 07:39:43,787] [INFO] Running command: hmmsearch --tblout GCA_020439245.1_ASM2043924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee67c467-5a73-44a6-b1b4-c6218d86ee55/dqc_reference/reference_markers.hmm GCA_020439245.1_ASM2043924v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 07:39:44,042] [INFO] Task succeeded: HMMsearch
[2023-06-29 07:39:44,044] [INFO] Found 6/6 markers.
[2023-06-29 07:39:44,075] [INFO] Query marker FASTA was written to GCA_020439245.1_ASM2043924v1_genomic.fna/markers.fasta
[2023-06-29 07:39:44,076] [INFO] Task started: Blastn
[2023-06-29 07:39:44,076] [INFO] Running command: blastn -query GCA_020439245.1_ASM2043924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee67c467-5a73-44a6-b1b4-c6218d86ee55/dqc_reference/reference_markers.fasta -out GCA_020439245.1_ASM2043924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:39:44,868] [INFO] Task succeeded: Blastn
[2023-06-29 07:39:44,873] [INFO] Selected 26 target genomes.
[2023-06-29 07:39:44,873] [INFO] Target genome list was writen to GCA_020439245.1_ASM2043924v1_genomic.fna/target_genomes.txt
[2023-06-29 07:39:44,897] [INFO] Task started: fastANI
[2023-06-29 07:39:44,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg325e9ea4-2e89-414e-b34d-4a7b177e5968/GCA_020439245.1_ASM2043924v1_genomic.fna.gz --refList GCA_020439245.1_ASM2043924v1_genomic.fna/target_genomes.txt --output GCA_020439245.1_ASM2043924v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 07:40:07,660] [INFO] Task succeeded: fastANI
[2023-06-29 07:40:07,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee67c467-5a73-44a6-b1b4-c6218d86ee55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 07:40:07,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee67c467-5a73-44a6-b1b4-c6218d86ee55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 07:40:07,687] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 07:40:07,687] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 07:40:07,688] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.4059	293	956	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.2749	290	956	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	77.0805	201	956	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.1595	265	956	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.1298	212	956	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	75.5281	228	956	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	75.5233	68	956	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	75.5109	158	956	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	75.4905	226	956	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	75.4668	156	956	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	75.4641	222	956	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	75.4212	158	956	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	75.4102	163	956	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	75.3526	183	956	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	75.3163	136	956	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	75.3144	196	956	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	75.3086	184	956	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	75.3027	220	956	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	75.297	179	956	95	below_threshold
Mobilicoccus massiliensis	strain=SIT2	GCA_000826525.2	1522310	1522310	type	True	75.2954	112	956	95	below_threshold
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	75.288	227	956	95	below_threshold
Williamsia deligens	strain=DSM 44902	GCA_024171765.1	321325	321325	type	True	75.2522	124	956	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	75.2267	220	956	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	75.155	213	956	95	below_threshold
Agromyces binzhouensis	strain=CGMCC 4.7180	GCA_004135055.1	1817495	1817495	type	True	75.1523	90	956	95	below_threshold
Agromyces kandeliae	strain=Q22	GCA_009674665.1	2666141	2666141	type	True	74.9145	123	956	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 07:40:07,705] [INFO] DFAST Taxonomy check result was written to GCA_020439245.1_ASM2043924v1_genomic.fna/tc_result.tsv
[2023-06-29 07:40:07,706] [INFO] ===== Taxonomy check completed =====
[2023-06-29 07:40:07,707] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 07:40:07,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee67c467-5a73-44a6-b1b4-c6218d86ee55/dqc_reference/checkm_data
[2023-06-29 07:40:07,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 07:40:07,748] [INFO] Task started: CheckM
[2023-06-29 07:40:07,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020439245.1_ASM2043924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020439245.1_ASM2043924v1_genomic.fna/checkm_input GCA_020439245.1_ASM2043924v1_genomic.fna/checkm_result
[2023-06-29 07:40:53,777] [INFO] Task succeeded: CheckM
[2023-06-29 07:40:53,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 2.15%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 07:40:53,805] [INFO] ===== Completeness check finished =====
[2023-06-29 07:40:53,805] [INFO] ===== Start GTDB Search =====
[2023-06-29 07:40:53,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020439245.1_ASM2043924v1_genomic.fna/markers.fasta)
[2023-06-29 07:40:53,806] [INFO] Task started: Blastn
[2023-06-29 07:40:53,806] [INFO] Running command: blastn -query GCA_020439245.1_ASM2043924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee67c467-5a73-44a6-b1b4-c6218d86ee55/dqc_reference/reference_markers_gtdb.fasta -out GCA_020439245.1_ASM2043924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:40:54,950] [INFO] Task succeeded: Blastn
[2023-06-29 07:40:54,955] [INFO] Selected 18 target genomes.
[2023-06-29 07:40:54,956] [INFO] Target genome list was writen to GCA_020439245.1_ASM2043924v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 07:40:54,962] [INFO] Task started: fastANI
[2023-06-29 07:40:54,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg325e9ea4-2e89-414e-b34d-4a7b177e5968/GCA_020439245.1_ASM2043924v1_genomic.fna.gz --refList GCA_020439245.1_ASM2043924v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020439245.1_ASM2043924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 07:41:06,226] [INFO] Task succeeded: fastANI
[2023-06-29 07:41:06,241] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 07:41:06,241] [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_003962875.1	s__AWTP1-35 sp003962875	97.7664	677	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018268735.1	s__AWTP1-35 sp018268735	81.5419	358	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	79.4693	415	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_903941145.1	s__CAJANQ01 sp903941145	79.142	281	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	98.35	98.35	0.80	0.80	2	-
GCA_903953195.1	s__SXMI01 sp903953195	78.8545	318	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	98.58	98.55	0.81	0.80	3	-
GCA_903930035.1	s__CAJANQ01 sp903930035	78.6892	242	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118345.1	s__SKRR01 sp007118345	78.5418	328	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SKRR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903852755.1	s__SXMI01 sp903852755	78.3412	352	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.71	99.61	0.93	0.92	10	-
GCA_005777415.1	s__SXMI01 sp005777415	77.782	261	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.41	99.40	0.88	0.87	3	-
GCF_019048865.1	s__Aquihabitans sp019048865	77.38	356	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	77.3129	319	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	77.2834	291	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703525.1	s__JADJBW01 sp016703525	77.0558	274	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__JADJBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719385.1	s__Microthrix sp002473265	77.0131	237	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__Microthrix	95.0	98.81	98.46	0.90	0.86	7	-
GCA_014381945.1	s__S20-B6 sp014381945	76.6674	153	956	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012841845.1	s__Dietzia sp012841845	75.7318	86	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034205.1	s__Streptomyces sp012034205	75.4004	167	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198655.1	s__R-H-3 sp002198655	75.1837	261	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 07:41:06,244] [INFO] GTDB search result was written to GCA_020439245.1_ASM2043924v1_genomic.fna/result_gtdb.tsv
[2023-06-29 07:41:06,244] [INFO] ===== GTDB Search completed =====
[2023-06-29 07:41:06,249] [INFO] DFAST_QC result json was written to GCA_020439245.1_ASM2043924v1_genomic.fna/dqc_result.json
[2023-06-29 07:41:06,249] [INFO] DFAST_QC completed!
[2023-06-29 07:41:06,249] [INFO] Total running time: 0h1m34s