[2024-01-24 12:14:33,710] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg332990f0-1969-4ae6-a38e-9fae3942486d/dqc_reference
[2024-01-24 12:14:35,162] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,163] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,163] [INFO] Running command: gunzip -c /var/lib/cwl/stgee8cd805-10e8-4114-baf6-485f0d340efc/GCF_002995495.1_ASM299549v1_genomic.fna.gz | prodigal -d GCF_002995495.1_ASM299549v1_genomic.fna/cds.fna -a GCF_002995495.1_ASM299549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:54,837] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:54,838] [INFO] Task started: HMMsearch
[2024-01-24 12:14:54,838] [INFO] Running command: hmmsearch --tblout GCF_002995495.1_ASM299549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg332990f0-1969-4ae6-a38e-9fae3942486d/dqc_reference/reference_markers.hmm GCF_002995495.1_ASM299549v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:55,151] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:55,152] [INFO] Found 6/6 markers.
[2024-01-24 12:14:55,224] [INFO] Query marker FASTA was written to GCF_002995495.1_ASM299549v1_genomic.fna/markers.fasta
[2024-01-24 12:14:55,224] [INFO] Task started: Blastn
[2024-01-24 12:14:55,225] [INFO] Running command: blastn -query GCF_002995495.1_ASM299549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg332990f0-1969-4ae6-a38e-9fae3942486d/dqc_reference/reference_markers.fasta -out GCF_002995495.1_ASM299549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:56,504] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:56,507] [INFO] Selected 25 target genomes.
[2024-01-24 12:14:56,507] [INFO] Target genome list was writen to GCF_002995495.1_ASM299549v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:56,513] [INFO] Task started: fastANI
[2024-01-24 12:14:56,513] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8cd805-10e8-4114-baf6-485f0d340efc/GCF_002995495.1_ASM299549v1_genomic.fna.gz --refList GCF_002995495.1_ASM299549v1_genomic.fna/target_genomes.txt --output GCF_002995495.1_ASM299549v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:41,952] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:41,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg332990f0-1969-4ae6-a38e-9fae3942486d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:41,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg332990f0-1969-4ae6-a38e-9fae3942486d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:41,966] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:41,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:41,967] [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
Actinocorallia herbida	strain=DSM 44254	GCA_003751225.1	58109	58109	type	True	81.6978	1534	2739	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	79.4356	911	2739	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	79.3604	893	2739	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	79.2997	1196	2739	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	79.2266	1221	2739	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	79.1972	1221	2739	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	79.1959	1130	2739	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	79.1576	924	2739	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	79.1442	1045	2739	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	79.1232	1151	2739	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	79.0334	1120	2739	95	below_threshold
Thermomonospora umbrina	strain=DSM 43927	GCA_003386555.1	111806	111806	type	True	79.0058	998	2739	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	78.9335	1087	2739	95	below_threshold
Actinomadura logoneensis	strain=NEAU-G17	GCA_003428695.1	2293572	2293572	type	True	78.9205	903	2739	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	78.8898	1069	2739	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	78.873	1234	2739	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	78.8469	1174	2739	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	78.8069	1243	2739	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	78.7694	1222	2739	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	78.5043	1064	2739	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	78.4924	998	2739	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	78.4529	1091	2739	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	78.3601	1030	2739	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	78.1481	865	2739	95	below_threshold
Actinoallomurus bryophytorum	strain=DSM 102200	GCA_006716425.1	1490222	1490222	type	True	77.8001	836	2739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,968] [INFO] DFAST Taxonomy check result was written to GCF_002995495.1_ASM299549v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:41,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:41,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:41,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg332990f0-1969-4ae6-a38e-9fae3942486d/dqc_reference/checkm_data
[2024-01-24 12:15:41,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:42,043] [INFO] Task started: CheckM
[2024-01-24 12:15:42,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002995495.1_ASM299549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002995495.1_ASM299549v1_genomic.fna/checkm_input GCF_002995495.1_ASM299549v1_genomic.fna/checkm_result
[2024-01-24 12:17:16,760] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:16,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:16,778] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:16,779] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:16,779] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002995495.1_ASM299549v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:16,779] [INFO] Task started: Blastn
[2024-01-24 12:17:16,779] [INFO] Running command: blastn -query GCF_002995495.1_ASM299549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg332990f0-1969-4ae6-a38e-9fae3942486d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002995495.1_ASM299549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:18,862] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:18,865] [INFO] Selected 19 target genomes.
[2024-01-24 12:17:18,865] [INFO] Target genome list was writen to GCF_002995495.1_ASM299549v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:18,874] [INFO] Task started: fastANI
[2024-01-24 12:17:18,874] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8cd805-10e8-4114-baf6-485f0d340efc/GCF_002995495.1_ASM299549v1_genomic.fna.gz --refList GCF_002995495.1_ASM299549v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002995495.1_ASM299549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:55,630] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:55,641] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:55,642] [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_002995495.1	s__Actinocorallia populi	100.0	2739	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinocorallia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003751225.1	s__Actinocorallia herbida	81.6757	1541	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinocorallia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108175.1	s__Thermomonospora echinospora	80.0253	1209	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003589885.1	s__Thermomonospora amylolytica	79.6318	1077	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	98.39	98.39	0.92	0.92	2	-
GCF_003289645.1	s__Actinomadura_D craniellae	79.4638	1079	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006363815.1	s__Thermomonospora catenispora	79.3472	896	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751755.1	s__Spirillospora viridis	79.1966	1130	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889745.1	s__Spirillospora geliboluensis	79.1315	1048	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001795.1	s__Actinomadura_B viridilutea	79.0968	976	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013364275.1	s__Spirillospora sp013364275	79.0129	1221	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824145.1	s__Spirillospora sp008824145	78.9934	1173	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386555.1	s__Thermomonospora umbrina	78.9914	1003	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409365.1	s__Spirillospora luteofluorescens	78.9145	1136	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017573545.1	s__Spirillospora nitritigenes	78.8452	1230	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_013211575.1	s__Spirillospora verrucosospora	78.7884	1259	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_008923365.1	s__Spirillospora montaniterrae	78.7868	1220	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659635.1	s__Spirillospora roseirufa	78.5308	961	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518265.1	s__Spirillospora oligospora	78.5195	1058	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009793335.1	s__Spirillospora sp009793335	78.5101	1190	2739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:55,643] [INFO] GTDB search result was written to GCF_002995495.1_ASM299549v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:55,644] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:55,647] [INFO] DFAST_QC result json was written to GCF_002995495.1_ASM299549v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:55,648] [INFO] DFAST_QC completed!
[2024-01-24 12:17:55,648] [INFO] Total running time: 0h3m22s