[2024-01-24 13:27:44,569] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:44,571] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:44,571] [INFO] DQC Reference Directory: /var/lib/cwl/stg650139b8-a4ad-44f3-bb1f-a9e75ad27fca/dqc_reference
[2024-01-24 13:27:45,869] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:45,870] [INFO] Task started: Prodigal
[2024-01-24 13:27:45,870] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0ea203a-a95c-4c4e-a586-e1c85f17c3f4/GCF_021556455.1_ASM2155645v1_genomic.fna.gz | prodigal -d GCF_021556455.1_ASM2155645v1_genomic.fna/cds.fna -a GCF_021556455.1_ASM2155645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:02,092] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:02,092] [INFO] Task started: HMMsearch
[2024-01-24 13:28:02,092] [INFO] Running command: hmmsearch --tblout GCF_021556455.1_ASM2155645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg650139b8-a4ad-44f3-bb1f-a9e75ad27fca/dqc_reference/reference_markers.hmm GCF_021556455.1_ASM2155645v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:02,482] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:02,483] [INFO] Found 6/6 markers.
[2024-01-24 13:28:02,534] [INFO] Query marker FASTA was written to GCF_021556455.1_ASM2155645v1_genomic.fna/markers.fasta
[2024-01-24 13:28:02,534] [INFO] Task started: Blastn
[2024-01-24 13:28:02,535] [INFO] Running command: blastn -query GCF_021556455.1_ASM2155645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg650139b8-a4ad-44f3-bb1f-a9e75ad27fca/dqc_reference/reference_markers.fasta -out GCF_021556455.1_ASM2155645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:03,865] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:03,868] [INFO] Selected 25 target genomes.
[2024-01-24 13:28:03,869] [INFO] Target genome list was writen to GCF_021556455.1_ASM2155645v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:03,879] [INFO] Task started: fastANI
[2024-01-24 13:28:03,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0ea203a-a95c-4c4e-a586-e1c85f17c3f4/GCF_021556455.1_ASM2155645v1_genomic.fna.gz --refList GCF_021556455.1_ASM2155645v1_genomic.fna/target_genomes.txt --output GCF_021556455.1_ASM2155645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:41,492] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:41,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg650139b8-a4ad-44f3-bb1f-a9e75ad27fca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:41,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg650139b8-a4ad-44f3-bb1f-a9e75ad27fca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:41,515] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:41,515] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:41,515] [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
Streptomyces fuscigenes	strain=JBL-20	GCA_021556455.1	1528880	1528880	type	True	100.0	1685	1705	95	conclusive
Streptomyces montanisoli	strain=MMS17-BM035	GCA_017813245.1	2798581	2798581	type	True	85.2236	1125	1705	95	below_threshold
Streptomyces liangshanensis	strain=QMT-12	GCA_011694815.1	2717324	2717324	type	True	81.8236	993	1705	95	below_threshold
Streptomyces scopuliridis	strain=RB72	GCA_003073355.1	452529	452529	type	True	81.5939	913	1705	95	below_threshold
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	81.5404	941	1705	95	below_threshold
Streptomyces lushanensis	strain=NRRL B-24994	GCA_001700515.1	1434255	1434255	type	True	81.4372	847	1705	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	81.395	802	1705	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	81.3912	871	1705	95	below_threshold
Streptomyces violascens	strain=NBRC 12920	GCA_020521295.1	67381	67381	type	True	81.3265	901	1705	95	below_threshold
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	81.3033	904	1705	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	81.2371	866	1705	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	81.1571	948	1705	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.1251	876	1705	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	81.0991	925	1705	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	81.02	949	1705	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.8819	913	1705	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	80.7617	917	1705	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	80.7297	864	1705	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	80.5915	836	1705	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	80.3926	940	1705	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	80.2394	913	1705	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	80.2315	723	1705	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.7576	725	1705	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	78.0075	671	1705	95	below_threshold
Actinocrinis puniceicyclus	strain=DSM 45618	GCA_018283645.1	977794	977794	type	True	76.862	438	1705	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:41,517] [INFO] DFAST Taxonomy check result was written to GCF_021556455.1_ASM2155645v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:41,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:41,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:41,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg650139b8-a4ad-44f3-bb1f-a9e75ad27fca/dqc_reference/checkm_data
[2024-01-24 13:28:41,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:41,586] [INFO] Task started: CheckM
[2024-01-24 13:28:41,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021556455.1_ASM2155645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021556455.1_ASM2155645v1_genomic.fna/checkm_input GCF_021556455.1_ASM2155645v1_genomic.fna/checkm_result
[2024-01-24 13:29:30,133] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:30,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:30,165] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:30,165] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:30,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021556455.1_ASM2155645v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:30,166] [INFO] Task started: Blastn
[2024-01-24 13:29:30,166] [INFO] Running command: blastn -query GCF_021556455.1_ASM2155645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg650139b8-a4ad-44f3-bb1f-a9e75ad27fca/dqc_reference/reference_markers_gtdb.fasta -out GCF_021556455.1_ASM2155645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:32,384] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:32,388] [INFO] Selected 27 target genomes.
[2024-01-24 13:29:32,389] [INFO] Target genome list was writen to GCF_021556455.1_ASM2155645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:32,435] [INFO] Task started: fastANI
[2024-01-24 13:29:32,436] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0ea203a-a95c-4c4e-a586-e1c85f17c3f4/GCF_021556455.1_ASM2155645v1_genomic.fna.gz --refList GCF_021556455.1_ASM2155645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021556455.1_ASM2155645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:15,469] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:15,495] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:30:15,496] [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
GCF_017813245.1	s__Streptomyces bomunensis	85.2412	1123	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721265.1	s__Streptomyces sp000721265	85.2041	1172	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000818175.1	s__Streptomyces sp000818175	82.2316	1050	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718095.1	s__Streptomyces scopuliridis	81.5581	939	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	81.5175	877	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCF_005981925.1	s__Streptomyces albidochromogenes	81.471	821	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	N/A	N/A	N/A	N/A	1	-
GCF_000719775.1	s__Streptomyces sp000719775	81.4224	958	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648195.1	s__Streptomyces purpureus	81.3943	871	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	99.54	0.95	0.95	2	-
GCF_003248355.1	s__Streptomyces sp003248355	81.3875	892	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.97	0.97	2	-
GCF_000981895.1	s__Streptomyces odonnellii	81.3439	889	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.86	95.86	0.85	0.85	2	-
GCF_001905905.1	s__Streptomyces sp001905905	81.3276	906	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.31	99.31	0.95	0.95	2	-
GCF_001646665.1	s__Streptomyces albulus_A	81.3146	918	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002551245.1	s__Streptomyces sp002551245	81.3133	842	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377145.1	s__Streptomyces sp000377145	81.3083	892	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653515.1	s__Streptomyces sp001653515	81.3045	825	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008120935.1	s__Streptomyces sp008120935	81.2693	971	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002154345.1	s__Streptomyces fimicarius	81.2628	837	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.88	95.22	0.89	0.81	11	-
GCF_014649795.1	s__Streptomyces melanogenes	81.153	949	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_003386135.1	s__Streptomyces sp003386135	81.0921	951	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_900091725.1	s__Streptomyces sp900091725	81.0066	950	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002803075.1	s__Streptomyces sp002803075	80.683	886	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006540305.1	s__Streptomyces sp006540305	80.6696	903	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650335.1	s__Streptomyces hiroshimensis	80.5466	842	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650555.1	s__Streptomyces goshikiensis	80.5276	883	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	96.91	0.89	0.81	10	-
GCF_008042115.1	s__Streptomyces sp008042115	80.4919	970	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003032475.1	s__Streptomyces sp003032475	80.4585	885	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105755.1	s__Streptomyces sp900105755	80.4306	966	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:15,498] [INFO] GTDB search result was written to GCF_021556455.1_ASM2155645v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:15,498] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:15,503] [INFO] DFAST_QC result json was written to GCF_021556455.1_ASM2155645v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:15,504] [INFO] DFAST_QC completed!
[2024-01-24 13:30:15,504] [INFO] Total running time: 0h2m31s