[2023-06-16 20:34:59,329] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:34:59,333] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:34:59,333] [INFO] DQC Reference Directory: /var/lib/cwl/stg29cec030-ee9b-4e12-a4dc-eef08dbba456/dqc_reference
[2023-06-16 20:35:01,058] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:35:01,059] [INFO] Task started: Prodigal
[2023-06-16 20:35:01,060] [INFO] Running command: gunzip -c /var/lib/cwl/stgf042a569-e964-4be5-9c01-933e1fa1f826/GCA_009836065.1_ASM983606v1_genomic.fna.gz | prodigal -d GCA_009836065.1_ASM983606v1_genomic.fna/cds.fna -a GCA_009836065.1_ASM983606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:35:11,216] [INFO] Task succeeded: Prodigal
[2023-06-16 20:35:11,216] [INFO] Task started: HMMsearch
[2023-06-16 20:35:11,216] [INFO] Running command: hmmsearch --tblout GCA_009836065.1_ASM983606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29cec030-ee9b-4e12-a4dc-eef08dbba456/dqc_reference/reference_markers.hmm GCA_009836065.1_ASM983606v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:35:11,447] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:35:11,448] [INFO] Found 6/6 markers.
[2023-06-16 20:35:11,477] [INFO] Query marker FASTA was written to GCA_009836065.1_ASM983606v1_genomic.fna/markers.fasta
[2023-06-16 20:35:11,477] [INFO] Task started: Blastn
[2023-06-16 20:35:11,477] [INFO] Running command: blastn -query GCA_009836065.1_ASM983606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29cec030-ee9b-4e12-a4dc-eef08dbba456/dqc_reference/reference_markers.fasta -out GCA_009836065.1_ASM983606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:35:12,196] [INFO] Task succeeded: Blastn
[2023-06-16 20:35:12,199] [INFO] Selected 30 target genomes.
[2023-06-16 20:35:12,200] [INFO] Target genome list was writen to GCA_009836065.1_ASM983606v1_genomic.fna/target_genomes.txt
[2023-06-16 20:35:12,204] [INFO] Task started: fastANI
[2023-06-16 20:35:12,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgf042a569-e964-4be5-9c01-933e1fa1f826/GCA_009836065.1_ASM983606v1_genomic.fna.gz --refList GCA_009836065.1_ASM983606v1_genomic.fna/target_genomes.txt --output GCA_009836065.1_ASM983606v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:35:38,679] [INFO] Task succeeded: fastANI
[2023-06-16 20:35:38,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29cec030-ee9b-4e12-a4dc-eef08dbba456/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:35:38,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29cec030-ee9b-4e12-a4dc-eef08dbba456/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:35:38,690] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:35:38,690] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 20:35:38,690] [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	76.8102	168	1134	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.7997	109	1134	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.7154	133	1134	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.909	96	1134	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.4531	90	1134	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	75.2967	67	1134	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	75.2019	60	1134	95	below_threshold
Quadrisphaera setariae	strain=DD2A	GCA_008041935.1	2593304	2593304	type	True	75.1166	62	1134	95	below_threshold
Amycolatopsis cihanbeyliensis	strain=DSM 45679	GCA_006715045.1	1128664	1128664	type	True	75.0896	60	1134	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	75.0846	68	1134	95	below_threshold
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	74.9966	75	1134	95	below_threshold
Streptomyces griseolus	strain=NRRL B-2925	GCA_000721185.1	1909	1909	type	True	74.9945	58	1134	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	74.9821	75	1134	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	74.9312	63	1134	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	74.6105	53	1134	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:35:38,691] [INFO] DFAST Taxonomy check result was written to GCA_009836065.1_ASM983606v1_genomic.fna/tc_result.tsv
[2023-06-16 20:35:38,692] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:35:38,692] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:35:38,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29cec030-ee9b-4e12-a4dc-eef08dbba456/dqc_reference/checkm_data
[2023-06-16 20:35:38,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:35:38,728] [INFO] Task started: CheckM
[2023-06-16 20:35:38,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009836065.1_ASM983606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009836065.1_ASM983606v1_genomic.fna/checkm_input GCA_009836065.1_ASM983606v1_genomic.fna/checkm_result
[2023-06-16 20:36:09,432] [INFO] Task succeeded: CheckM
[2023-06-16 20:36:09,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 20:36:09,450] [INFO] ===== Completeness check finished =====
[2023-06-16 20:36:09,450] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:36:09,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009836065.1_ASM983606v1_genomic.fna/markers.fasta)
[2023-06-16 20:36:09,450] [INFO] Task started: Blastn
[2023-06-16 20:36:09,450] [INFO] Running command: blastn -query GCA_009836065.1_ASM983606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29cec030-ee9b-4e12-a4dc-eef08dbba456/dqc_reference/reference_markers_gtdb.fasta -out GCA_009836065.1_ASM983606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:36:10,476] [INFO] Task succeeded: Blastn
[2023-06-16 20:36:10,479] [INFO] Selected 18 target genomes.
[2023-06-16 20:36:10,479] [INFO] Target genome list was writen to GCA_009836065.1_ASM983606v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:36:10,483] [INFO] Task started: fastANI
[2023-06-16 20:36:10,483] [INFO] Running command: fastANI --query /var/lib/cwl/stgf042a569-e964-4be5-9c01-933e1fa1f826/GCA_009836065.1_ASM983606v1_genomic.fna.gz --refList GCA_009836065.1_ASM983606v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009836065.1_ASM983606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:36:23,224] [INFO] Task succeeded: fastANI
[2023-06-16 20:36:23,235] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 20:36:23,236] [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_009842675.1	s__Bin134 sp009842675	96.6775	956	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__Bin134	95.0	96.86	96.18	0.91	0.88	13	conclusive
GCA_009843565.1	s__Bin134 sp009843565	85.8448	395	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__Bin134	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002239105.1	s__Bin134 sp002239105	84.3213	850	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__Bin134	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346745.1	s__S20-B6 sp002346745	77.3383	127	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_016845305.1	s__UBA9410 sp016845305	77.2878	165	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840735.1	s__VXNF01 sp009840735	77.0808	153	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__VXNF01	95.0	98.98	98.92	0.89	0.88	3	-
GCF_014805525.1	s__Rhabdothermincola sediminis	76.7997	109	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__Rhabdothermincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	76.7303	132	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121465.1	s__SKKL01 sp007121465	76.6141	102	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__SKKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	76.5863	187	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	76.4128	157	1134	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	76.3638	145	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649895.1	s__Actinomarinicola sp016649895	76.3551	113	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	76.1708	110	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.1507	129	1134	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCF_006715045.1	s__Amycolatopsis_D cihanbeyliensis	75.0896	60	1134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096675.1	s__Actinomycetospora cinnamomea	74.9966	75	1134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377205.1	s__Streptomyces phyllanthi	74.9884	74	1134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 20:36:23,238] [INFO] GTDB search result was written to GCA_009836065.1_ASM983606v1_genomic.fna/result_gtdb.tsv
[2023-06-16 20:36:23,239] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:36:23,242] [INFO] DFAST_QC result json was written to GCA_009836065.1_ASM983606v1_genomic.fna/dqc_result.json
[2023-06-16 20:36:23,242] [INFO] DFAST_QC completed!
[2023-06-16 20:36:23,242] [INFO] Total running time: 0h1m24s