[2023-06-27 06:11:07,991] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:11:07,992] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:11:07,992] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f14b756-c3e2-4640-bee1-53c2cf4c40f8/dqc_reference
[2023-06-27 06:11:09,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:11:09,275] [INFO] Task started: Prodigal
[2023-06-27 06:11:09,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b3649fc-959d-42ed-ba7c-2cc41a649e86/GCA_026708015.1_ASM2670801v1_genomic.fna.gz | prodigal -d GCA_026708015.1_ASM2670801v1_genomic.fna/cds.fna -a GCA_026708015.1_ASM2670801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:11:20,449] [INFO] Task succeeded: Prodigal
[2023-06-27 06:11:20,450] [INFO] Task started: HMMsearch
[2023-06-27 06:11:20,450] [INFO] Running command: hmmsearch --tblout GCA_026708015.1_ASM2670801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f14b756-c3e2-4640-bee1-53c2cf4c40f8/dqc_reference/reference_markers.hmm GCA_026708015.1_ASM2670801v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:11:20,663] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:11:20,664] [INFO] Found 6/6 markers.
[2023-06-27 06:11:20,719] [INFO] Query marker FASTA was written to GCA_026708015.1_ASM2670801v1_genomic.fna/markers.fasta
[2023-06-27 06:11:20,720] [INFO] Task started: Blastn
[2023-06-27 06:11:20,720] [INFO] Running command: blastn -query GCA_026708015.1_ASM2670801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f14b756-c3e2-4640-bee1-53c2cf4c40f8/dqc_reference/reference_markers.fasta -out GCA_026708015.1_ASM2670801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:11:21,404] [INFO] Task succeeded: Blastn
[2023-06-27 06:11:21,408] [INFO] Selected 29 target genomes.
[2023-06-27 06:11:21,408] [INFO] Target genome list was writen to GCA_026708015.1_ASM2670801v1_genomic.fna/target_genomes.txt
[2023-06-27 06:11:21,413] [INFO] Task started: fastANI
[2023-06-27 06:11:21,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b3649fc-959d-42ed-ba7c-2cc41a649e86/GCA_026708015.1_ASM2670801v1_genomic.fna.gz --refList GCA_026708015.1_ASM2670801v1_genomic.fna/target_genomes.txt --output GCA_026708015.1_ASM2670801v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:11:46,940] [INFO] Task succeeded: fastANI
[2023-06-27 06:11:46,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f14b756-c3e2-4640-bee1-53c2cf4c40f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:11:46,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f14b756-c3e2-4640-bee1-53c2cf4c40f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:11:46,955] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:11:46,955] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:11:46,955] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.0	133	1130	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.8397	169	1130	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.7505	127	1130	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.1053	52	1130	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.054	90	1130	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.0486	105	1130	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	75.432	72	1130	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	75.4218	86	1130	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	75.4064	61	1130	95	below_threshold
Streptomyces reniochalinae	strain=LHW50302	GCA_003323735.1	2250578	2250578	type	True	75.3728	75	1130	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	75.3357	63	1130	95	below_threshold
Nocardia aurantia	strain=RB56	GCA_009604425.1	2585199	2585199	type	True	75.2816	60	1130	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	75.2263	71	1130	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	75.119	86	1130	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	75.0706	110	1130	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	75.0268	82	1130	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	74.9725	91	1130	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:11:46,957] [INFO] DFAST Taxonomy check result was written to GCA_026708015.1_ASM2670801v1_genomic.fna/tc_result.tsv
[2023-06-27 06:11:46,958] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:11:46,958] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:11:46,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f14b756-c3e2-4640-bee1-53c2cf4c40f8/dqc_reference/checkm_data
[2023-06-27 06:11:46,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:11:47,030] [INFO] Task started: CheckM
[2023-06-27 06:11:47,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708015.1_ASM2670801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708015.1_ASM2670801v1_genomic.fna/checkm_input GCA_026708015.1_ASM2670801v1_genomic.fna/checkm_result
[2023-06-27 06:12:21,886] [INFO] Task succeeded: CheckM
[2023-06-27 06:12:21,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:12:21,900] [INFO] ===== Completeness check finished =====
[2023-06-27 06:12:21,900] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:12:21,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708015.1_ASM2670801v1_genomic.fna/markers.fasta)
[2023-06-27 06:12:21,901] [INFO] Task started: Blastn
[2023-06-27 06:12:21,901] [INFO] Running command: blastn -query GCA_026708015.1_ASM2670801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f14b756-c3e2-4640-bee1-53c2cf4c40f8/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708015.1_ASM2670801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:12:22,826] [INFO] Task succeeded: Blastn
[2023-06-27 06:12:22,829] [INFO] Selected 21 target genomes.
[2023-06-27 06:12:22,829] [INFO] Target genome list was writen to GCA_026708015.1_ASM2670801v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:12:22,857] [INFO] Task started: fastANI
[2023-06-27 06:12:22,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b3649fc-959d-42ed-ba7c-2cc41a649e86/GCA_026708015.1_ASM2670801v1_genomic.fna.gz --refList GCA_026708015.1_ASM2670801v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708015.1_ASM2670801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:12:35,210] [INFO] Task succeeded: fastANI
[2023-06-27 06:12:35,226] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:12:35,226] [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	90.8841	866	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__Bin134	95.0	96.86	96.18	0.91	0.88	13	-
GCA_009843565.1	s__Bin134 sp009843565	85.4597	394	1130	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	84.363	816	1130	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	77.2372	144	1130	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_009835735.1	s__VYCW01 sp009835735	77.1543	171	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.69	99.63	0.88	0.85	3	-
GCA_002861595.1	s__GCA-2861595 sp002861595	77.0916	90	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__GCA-2861595;g__GCA-2861595	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	77.0004	133	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727895.1	s__UBA9410 sp002727895	76.8862	123	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_012961035.1	s__UBA9410 sp012961035	76.885	111	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_014381945.1	s__S20-B6 sp014381945	76.7935	130	1130	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	-
GCF_014805525.1	s__Rhabdothermincola sediminis	76.7505	127	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__Rhabdothermincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	76.7179	189	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	76.6512	143	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	76.5774	145	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513855.1	s__JAAZBK01 sp012513855	76.4655	104	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAZBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	76.4492	111	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	76.4398	178	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826025.1	s__CADEDH01 sp902826025	76.4148	200	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SZUA-35;g__CADEDH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003962875.1	s__AWTP1-35 sp003962875	76.4132	88	1130	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323715.1	s__Streptomyces diacarni	75.4302	72	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:12:35,228] [INFO] GTDB search result was written to GCA_026708015.1_ASM2670801v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:12:35,228] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:12:35,232] [INFO] DFAST_QC result json was written to GCA_026708015.1_ASM2670801v1_genomic.fna/dqc_result.json
[2023-06-27 06:12:35,232] [INFO] DFAST_QC completed!
[2023-06-27 06:12:35,232] [INFO] Total running time: 0h1m27s