[2024-01-25 19:36:50,641] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:50,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:50,642] [INFO] DQC Reference Directory: /var/lib/cwl/stgff142ff4-5d35-44de-90cb-e80e719063ea/dqc_reference
[2024-01-25 19:36:51,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:51,779] [INFO] Task started: Prodigal
[2024-01-25 19:36:51,779] [INFO] Running command: gunzip -c /var/lib/cwl/stg055a2f2a-750a-40d8-a027-a999b74bb0df/GCF_001445835.1_ASM144583v1_genomic.fna.gz | prodigal -d GCF_001445835.1_ASM144583v1_genomic.fna/cds.fna -a GCF_001445835.1_ASM144583v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:09,198] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:09,198] [INFO] Task started: HMMsearch
[2024-01-25 19:37:09,198] [INFO] Running command: hmmsearch --tblout GCF_001445835.1_ASM144583v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff142ff4-5d35-44de-90cb-e80e719063ea/dqc_reference/reference_markers.hmm GCF_001445835.1_ASM144583v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:09,516] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:09,517] [INFO] Found 6/6 markers.
[2024-01-25 19:37:09,574] [INFO] Query marker FASTA was written to GCF_001445835.1_ASM144583v1_genomic.fna/markers.fasta
[2024-01-25 19:37:09,575] [INFO] Task started: Blastn
[2024-01-25 19:37:09,575] [INFO] Running command: blastn -query GCF_001445835.1_ASM144583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff142ff4-5d35-44de-90cb-e80e719063ea/dqc_reference/reference_markers.fasta -out GCF_001445835.1_ASM144583v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:10,792] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:10,796] [INFO] Selected 22 target genomes.
[2024-01-25 19:37:10,796] [INFO] Target genome list was writen to GCF_001445835.1_ASM144583v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:10,807] [INFO] Task started: fastANI
[2024-01-25 19:37:10,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg055a2f2a-750a-40d8-a027-a999b74bb0df/GCF_001445835.1_ASM144583v1_genomic.fna.gz --refList GCF_001445835.1_ASM144583v1_genomic.fna/target_genomes.txt --output GCF_001445835.1_ASM144583v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:44,456] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:44,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff142ff4-5d35-44de-90cb-e80e719063ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:44,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff142ff4-5d35-44de-90cb-e80e719063ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:44,469] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:37:44,469] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:44,469] [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
Wenjunlia vitaminophila	strain=ATCC 31673	GCA_001445835.1	76728	76728	type	True	100.0	2157	2164	95	conclusive
Wenjunlia vitaminophila	strain=DSM 41686	GCA_000380165.1	76728	76728	type	True	99.8974	2056	2164	95	conclusive
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	79.7554	836	2164	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	79.6828	830	2164	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.4138	825	2164	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	79.3474	891	2164	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	79.2491	804	2164	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	79.1468	818	2164	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	79.0628	836	2164	95	below_threshold
Peterkaempfera bronchialis	strain=DSM 106435	GCA_003258605.2	2126346	2126346	type	True	79.0555	852	2164	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	79.0166	871	2164	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	79.0124	870	2164	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	78.9965	787	2164	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	78.9939	879	2164	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	78.8896	780	2164	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	78.8261	846	2164	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	78.7118	917	2164	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	78.7117	826	2164	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	78.6434	808	2164	95	below_threshold
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	78.6375	807	2164	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	78.535	849	2164	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	78.2807	879	2164	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:44,471] [INFO] DFAST Taxonomy check result was written to GCF_001445835.1_ASM144583v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:44,472] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:44,472] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:44,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff142ff4-5d35-44de-90cb-e80e719063ea/dqc_reference/checkm_data
[2024-01-25 19:37:44,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:44,535] [INFO] Task started: CheckM
[2024-01-25 19:37:44,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001445835.1_ASM144583v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001445835.1_ASM144583v1_genomic.fna/checkm_input GCF_001445835.1_ASM144583v1_genomic.fna/checkm_result
[2024-01-25 19:39:09,406] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:09,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:09,428] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:09,428] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:09,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001445835.1_ASM144583v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:09,429] [INFO] Task started: Blastn
[2024-01-25 19:39:09,429] [INFO] Running command: blastn -query GCF_001445835.1_ASM144583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff142ff4-5d35-44de-90cb-e80e719063ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_001445835.1_ASM144583v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:11,427] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:11,430] [INFO] Selected 24 target genomes.
[2024-01-25 19:39:11,430] [INFO] Target genome list was writen to GCF_001445835.1_ASM144583v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:11,470] [INFO] Task started: fastANI
[2024-01-25 19:39:11,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg055a2f2a-750a-40d8-a027-a999b74bb0df/GCF_001445835.1_ASM144583v1_genomic.fna.gz --refList GCF_001445835.1_ASM144583v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001445835.1_ASM144583v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:50,528] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:50,542] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:50,542] [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_000380165.1	s__Streptomyces_A vitaminophilus	99.8974	2056	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_A	95.0	99.94	99.94	0.99	0.99	2	conclusive
GCF_014646055.1	s__Streptomyces_A tyrosinilyticus	80.5338	1010	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083985.1	s__SCUT-3 sp014083985	79.855	904	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__SCUT-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003144095.1	s__Streptomyces sp003144095	79.8073	828	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684805.1	s__Streptomyces palmae	79.7992	830	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000240165.1	s__Streptomyces cattleya	79.7569	960	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	3	-
GCF_017114865.1	s__Streptomyces verrucosisporus	79.3766	860	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_900110735.1	s__Streptomyces radiopugnans	79.3366	893	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258605.2	s__Streptomyces_D bronchialis	79.0131	860	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553455.1	s__Streptomyces hygroscopicus	79.0018	872	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
GCF_016916835.1	s__Streptomyces bryophytorum	79.0003	885	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_017916255.1	s__Streptomyces mobaraensis	78.9754	868	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
GCF_000761215.1	s__Streptomyces glaucescens	78.9194	916	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034935.1	s__Streptomyces sp012034935	78.9026	852	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248315.1	s__Streptomyces sp003248315	78.9006	910	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756395.1	s__Streptomyces sp016756395	78.8992	945	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018138715.1	s__Streptomyces asiaticus	78.8704	950	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_000701325.1	s__Streptomyces sp000701325	78.8445	869	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811555.1	s__Streptomyces caniferus	78.8205	845	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514125.1	s__Streptomyces longwoodensis	78.7949	921	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_014649115.1	s__Streptomyces eurythermus	78.7737	943	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_900111245.1	s__Streptomyces qinglanensis	78.6403	807	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000424765.1	s__Streptomyces sp000424765	78.4843	842	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.13	98.98	0.93	0.92	5	-
GCF_000719095.1	s__Streptacidiphilus jeojiense	78.4338	822	2164	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:50,543] [INFO] GTDB search result was written to GCF_001445835.1_ASM144583v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:50,544] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:50,548] [INFO] DFAST_QC result json was written to GCF_001445835.1_ASM144583v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:50,548] [INFO] DFAST_QC completed!
[2024-01-25 19:39:50,548] [INFO] Total running time: 0h2m60s