[2023-06-28 16:48:38,540] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:48:38,542] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:48:38,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f748d65-2425-44d6-bb0e-dd25799147d8/dqc_reference
[2023-06-28 16:48:39,828] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:48:39,829] [INFO] Task started: Prodigal
[2023-06-28 16:48:39,830] [INFO] Running command: gunzip -c /var/lib/cwl/stgca583043-476b-4340-b792-ca37559a92b9/GCA_027396295.1_ASM2739629v1_genomic.fna.gz | prodigal -d GCA_027396295.1_ASM2739629v1_genomic.fna/cds.fna -a GCA_027396295.1_ASM2739629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:48:48,350] [INFO] Task succeeded: Prodigal
[2023-06-28 16:48:48,350] [INFO] Task started: HMMsearch
[2023-06-28 16:48:48,351] [INFO] Running command: hmmsearch --tblout GCA_027396295.1_ASM2739629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f748d65-2425-44d6-bb0e-dd25799147d8/dqc_reference/reference_markers.hmm GCA_027396295.1_ASM2739629v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:48:48,613] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:48:48,615] [INFO] Found 6/6 markers.
[2023-06-28 16:48:48,645] [INFO] Query marker FASTA was written to GCA_027396295.1_ASM2739629v1_genomic.fna/markers.fasta
[2023-06-28 16:48:48,645] [INFO] Task started: Blastn
[2023-06-28 16:48:48,646] [INFO] Running command: blastn -query GCA_027396295.1_ASM2739629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f748d65-2425-44d6-bb0e-dd25799147d8/dqc_reference/reference_markers.fasta -out GCA_027396295.1_ASM2739629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:48:49,403] [INFO] Task succeeded: Blastn
[2023-06-28 16:48:49,409] [INFO] Selected 25 target genomes.
[2023-06-28 16:48:49,410] [INFO] Target genome list was writen to GCA_027396295.1_ASM2739629v1_genomic.fna/target_genomes.txt
[2023-06-28 16:48:49,418] [INFO] Task started: fastANI
[2023-06-28 16:48:49,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgca583043-476b-4340-b792-ca37559a92b9/GCA_027396295.1_ASM2739629v1_genomic.fna.gz --refList GCA_027396295.1_ASM2739629v1_genomic.fna/target_genomes.txt --output GCA_027396295.1_ASM2739629v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:49:09,667] [INFO] Task succeeded: fastANI
[2023-06-28 16:49:09,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f748d65-2425-44d6-bb0e-dd25799147d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:49:09,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f748d65-2425-44d6-bb0e-dd25799147d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:49:09,684] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:49:09,684] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:49:09,684] [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	76.0174	156	957	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.9076	147	957	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	75.8954	113	957	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.6917	111	957	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.639	173	957	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	75.3998	95	957	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	75.3712	108	957	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	75.324	127	957	95	below_threshold
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	75.3121	171	957	95	below_threshold
Acrocarpospora corrugata	strain=NBRC 13972	GCA_009687845.1	35763	35763	type	True	75.214	102	957	95	below_threshold
Kibdelosporangium banguiense	strain=DSM 46670	GCA_017876405.1	1365924	1365924	type	True	75.1607	84	957	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	75.1573	137	957	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	75.0907	74	957	95	below_threshold
Pseudoclavibacter chungangensis	strain=DSM 23821	GCA_013410545.1	587635	587635	type	True	75.0337	88	957	95	below_threshold
Agromyces salentinus	strain=JCM 14323	GCA_009749395.1	269421	269421	type	True	75.0337	94	957	95	below_threshold
Stackebrandtia nassauensis	strain=DSM 44728	GCA_000024545.1	283811	283811	type	True	74.9777	91	957	95	below_threshold
Acrocarpospora macrocephala	strain=NBRC 16266	GCA_009687865.1	150177	150177	type	True	74.9742	123	957	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.9225	190	957	95	below_threshold
Amycolatopsis thermoflava	strain=N1165	GCA_000473265.1	84480	84480	type	True	74.9184	142	957	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:49:09,687] [INFO] DFAST Taxonomy check result was written to GCA_027396295.1_ASM2739629v1_genomic.fna/tc_result.tsv
[2023-06-28 16:49:09,687] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:49:09,688] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:49:09,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f748d65-2425-44d6-bb0e-dd25799147d8/dqc_reference/checkm_data
[2023-06-28 16:49:09,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:49:09,725] [INFO] Task started: CheckM
[2023-06-28 16:49:09,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027396295.1_ASM2739629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027396295.1_ASM2739629v1_genomic.fna/checkm_input GCA_027396295.1_ASM2739629v1_genomic.fna/checkm_result
[2023-06-28 16:49:40,167] [INFO] Task succeeded: CheckM
[2023-06-28 16:49:40,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:49:40,192] [INFO] ===== Completeness check finished =====
[2023-06-28 16:49:40,192] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:49:40,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027396295.1_ASM2739629v1_genomic.fna/markers.fasta)
[2023-06-28 16:49:40,193] [INFO] Task started: Blastn
[2023-06-28 16:49:40,193] [INFO] Running command: blastn -query GCA_027396295.1_ASM2739629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f748d65-2425-44d6-bb0e-dd25799147d8/dqc_reference/reference_markers_gtdb.fasta -out GCA_027396295.1_ASM2739629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:49:41,301] [INFO] Task succeeded: Blastn
[2023-06-28 16:49:41,307] [INFO] Selected 24 target genomes.
[2023-06-28 16:49:41,307] [INFO] Target genome list was writen to GCA_027396295.1_ASM2739629v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:49:41,318] [INFO] Task started: fastANI
[2023-06-28 16:49:41,318] [INFO] Running command: fastANI --query /var/lib/cwl/stgca583043-476b-4340-b792-ca37559a92b9/GCA_027396295.1_ASM2739629v1_genomic.fna.gz --refList GCA_027396295.1_ASM2739629v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027396295.1_ASM2739629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:49:54,373] [INFO] Task succeeded: fastANI
[2023-06-28 16:49:54,406] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:49:54,406] [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_003155135.1	s__Bog-515 sp003155135	77.7209	194	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-515	95.0	99.89	99.76	0.97	0.95	17	-
GCA_003161255.1	s__Palsa-461 sp003161255	77.2862	169	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Palsa-461	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003169235.1	s__Bog-473 sp003169235	77.2409	163	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-473	95.0	99.17	99.17	0.82	0.82	2	-
GCA_003153575.1	s__Bog-756 sp003153575	77.1126	123	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.41	99.41	0.75	0.75	2	-
GCA_003164095.1	s__Bog-756 sp003164095	77.0344	162	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151235.1	s__Palsa-461 sp003151235	77.0238	184	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Palsa-461	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133545.1	s__Bog-473 sp003133545	76.9266	133	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-473	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003453695.1	s__UBA8190 sp003453695	76.8795	146	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__UBA8190	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255565.1	s__RAAP-2 sp002255565	76.8011	120	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003162395.1	s__Palsa-459 sp003162395	76.7724	123	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Palsa-459	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003159795.1	s__Bog-793 sp003159795	76.7162	112	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Bog-793	95.0	99.80	99.71	0.91	0.89	3	-
GCA_003151955.1	s__PALSA-743 sp003151955	76.5794	152	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__PALSA-743	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135595.1	s__Palsa-459 sp003135595	76.5477	97	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Palsa-459	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888395.1	s__AC-25 sp005888395	76.4114	115	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-25;g__AC-25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888295.1	s__AC-9 sp005888295	76.3104	137	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__QHCF01;g__AC-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133325.1	s__Bog-756 sp003133325	76.2545	83	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.83	99.78	0.97	0.96	4	-
GCA_016649895.1	s__Actinomarinicola sp016649895	76.1699	117	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870475.1	s__VGBO01 sp016870475	76.0725	92	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CAIXPF01;g__VGBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	76.0164	156	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870595.1	s__CAIUKV01 sp016870595	75.8968	107	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164275.1	s__Bog-756 sp003164275	75.8833	71	957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096675.1	s__Actinomycetospora cinnamomea	75.3164	171	957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517965.1	s__Propioniciclava sp012517965	74.9978	72	957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propioniciclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425465.1	s__Methylobacterium sp001425465	74.7923	74	957	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:49:54,412] [INFO] GTDB search result was written to GCA_027396295.1_ASM2739629v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:49:54,412] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:49:54,417] [INFO] DFAST_QC result json was written to GCA_027396295.1_ASM2739629v1_genomic.fna/dqc_result.json
[2023-06-28 16:49:54,418] [INFO] DFAST_QC completed!
[2023-06-28 16:49:54,418] [INFO] Total running time: 0h1m16s