[2023-06-30 23:36:49,369] [INFO] DFAST_QC pipeline started.
[2023-06-30 23:36:49,370] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 23:36:49,371] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfde2631-ede7-4e59-b5af-ed1d325524a8/dqc_reference
[2023-06-30 23:36:52,666] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 23:36:52,667] [INFO] Task started: Prodigal
[2023-06-30 23:36:52,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d752342-d285-4463-8744-3b876531e0ed/GCA_016720545.1_ASM1672054v1_genomic.fna.gz | prodigal -d GCA_016720545.1_ASM1672054v1_genomic.fna/cds.fna -a GCA_016720545.1_ASM1672054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 23:37:13,126] [INFO] Task succeeded: Prodigal
[2023-06-30 23:37:13,127] [INFO] Task started: HMMsearch
[2023-06-30 23:37:13,127] [INFO] Running command: hmmsearch --tblout GCA_016720545.1_ASM1672054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfde2631-ede7-4e59-b5af-ed1d325524a8/dqc_reference/reference_markers.hmm GCA_016720545.1_ASM1672054v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 23:37:13,461] [INFO] Task succeeded: HMMsearch
[2023-06-30 23:37:13,462] [INFO] Found 6/6 markers.
[2023-06-30 23:37:13,520] [INFO] Query marker FASTA was written to GCA_016720545.1_ASM1672054v1_genomic.fna/markers.fasta
[2023-06-30 23:37:13,521] [INFO] Task started: Blastn
[2023-06-30 23:37:13,521] [INFO] Running command: blastn -query GCA_016720545.1_ASM1672054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfde2631-ede7-4e59-b5af-ed1d325524a8/dqc_reference/reference_markers.fasta -out GCA_016720545.1_ASM1672054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:37:14,231] [INFO] Task succeeded: Blastn
[2023-06-30 23:37:14,235] [INFO] Selected 28 target genomes.
[2023-06-30 23:37:14,235] [INFO] Target genome list was writen to GCA_016720545.1_ASM1672054v1_genomic.fna/target_genomes.txt
[2023-06-30 23:37:14,242] [INFO] Task started: fastANI
[2023-06-30 23:37:14,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d752342-d285-4463-8744-3b876531e0ed/GCA_016720545.1_ASM1672054v1_genomic.fna.gz --refList GCA_016720545.1_ASM1672054v1_genomic.fna/target_genomes.txt --output GCA_016720545.1_ASM1672054v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 23:37:44,039] [INFO] Task succeeded: fastANI
[2023-06-30 23:37:44,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfde2631-ede7-4e59-b5af-ed1d325524a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 23:37:44,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfde2631-ede7-4e59-b5af-ed1d325524a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 23:37:44,064] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 23:37:44,065] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 23:37:44,065] [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
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	76.8811	658	2459	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.7499	798	2459	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.6595	788	2459	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.6183	739	2459	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.5309	436	2459	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.3395	878	2459	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1841	489	2459	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	75.0116	94	2459	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	75.0096	139	2459	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.0082	695	2459	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	74.9678	174	2459	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	74.9577	91	2459	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.9555	681	2459	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	74.9179	123	2459	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	74.9173	173	2459	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	74.9121	207	2459	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	74.8911	122	2459	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	74.8728	210	2459	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	74.8331	215	2459	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	74.7895	92	2459	95	below_threshold
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	74.7768	210	2459	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	74.7767	95	2459	95	below_threshold
Streptomyces fagopyri	strain=QMT-28	GCA_009498275.1	2662397	2662397	type	True	74.7753	286	2459	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	74.7687	329	2459	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	74.7567	217	2459	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	74.7459	206	2459	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	74.7284	321	2459	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	74.7135	311	2459	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 23:37:44,067] [INFO] DFAST Taxonomy check result was written to GCA_016720545.1_ASM1672054v1_genomic.fna/tc_result.tsv
[2023-06-30 23:37:44,068] [INFO] ===== Taxonomy check completed =====
[2023-06-30 23:37:44,068] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 23:37:44,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfde2631-ede7-4e59-b5af-ed1d325524a8/dqc_reference/checkm_data
[2023-06-30 23:37:44,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 23:37:44,136] [INFO] Task started: CheckM
[2023-06-30 23:37:44,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016720545.1_ASM1672054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016720545.1_ASM1672054v1_genomic.fna/checkm_input GCA_016720545.1_ASM1672054v1_genomic.fna/checkm_result
[2023-06-30 23:38:43,677] [INFO] Task succeeded: CheckM
[2023-06-30 23:38:43,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 23:38:43,704] [INFO] ===== Completeness check finished =====
[2023-06-30 23:38:43,704] [INFO] ===== Start GTDB Search =====
[2023-06-30 23:38:43,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016720545.1_ASM1672054v1_genomic.fna/markers.fasta)
[2023-06-30 23:38:43,705] [INFO] Task started: Blastn
[2023-06-30 23:38:43,705] [INFO] Running command: blastn -query GCA_016720545.1_ASM1672054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfde2631-ede7-4e59-b5af-ed1d325524a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_016720545.1_ASM1672054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:38:44,812] [INFO] Task succeeded: Blastn
[2023-06-30 23:38:44,817] [INFO] Selected 13 target genomes.
[2023-06-30 23:38:44,817] [INFO] Target genome list was writen to GCA_016720545.1_ASM1672054v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 23:38:44,828] [INFO] Task started: fastANI
[2023-06-30 23:38:44,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d752342-d285-4463-8744-3b876531e0ed/GCA_016720545.1_ASM1672054v1_genomic.fna.gz --refList GCA_016720545.1_ASM1672054v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016720545.1_ASM1672054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 23:39:08,204] [INFO] Task succeeded: fastANI
[2023-06-30 23:39:08,217] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 23:39:08,217] [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_016720545.1	s__JAAFHV01 sp016720545	100.0	2455	2459	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	99.45	99.45	0.94	0.94	2	conclusive
GCA_016712525.1	s__JAAFHV01 sp016712525	79.2348	1256	2459	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297655.1	s__JAAFHV01 sp013297655	78.5595	1099	2459	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001263205.1	s__Labilithrix luteola	76.9246	654	2459	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899635.1	s__Labilithrix sp001899635	76.787	826	2459	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777185.1	s__SXNL01 sp005777185	76.5	662	2459	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__SXNL01	95.0	99.91	99.91	0.95	0.95	3	-
GCA_016703425.1	s__JADJCA01 sp016703425	76.2655	623	2459	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153495.1	s__Palsa-1150 sp003153495	76.0355	377	2459	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Palsa-1150	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709545.1	s__JADJMO01 sp016709545	75.965	793	2459	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJMO01;g__JADJMO01	95.0	95.09	95.09	0.90	0.90	2	-
GCF_002950945.1	s__Sorangium cellulosum_E	75.5522	951	2459	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009296025.1	s__Streptomyces tsukubensis_B	74.8267	230	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003814695.1	s__Myceligenerans xiligouense	74.8219	212	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280195.1	s__Streptomyces galbus	74.7318	329	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-30 23:39:08,220] [INFO] GTDB search result was written to GCA_016720545.1_ASM1672054v1_genomic.fna/result_gtdb.tsv
[2023-06-30 23:39:08,220] [INFO] ===== GTDB Search completed =====
[2023-06-30 23:39:08,225] [INFO] DFAST_QC result json was written to GCA_016720545.1_ASM1672054v1_genomic.fna/dqc_result.json
[2023-06-30 23:39:08,225] [INFO] DFAST_QC completed!
[2023-06-30 23:39:08,225] [INFO] Total running time: 0h2m19s