[2024-01-24 13:22:55,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:55,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:55,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e6fa8a0-4104-43f0-8eb8-07dc7acf661c/dqc_reference
[2024-01-24 13:22:56,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:56,694] [INFO] Task started: Prodigal
[2024-01-24 13:22:56,695] [INFO] Running command: gunzip -c /var/lib/cwl/stg3628e744-6978-4eb9-9641-68e586610213/GCF_007845645.1_ASM784564v1_genomic.fna.gz | prodigal -d GCF_007845645.1_ASM784564v1_genomic.fna/cds.fna -a GCF_007845645.1_ASM784564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:13,979] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:13,980] [INFO] Task started: HMMsearch
[2024-01-24 13:23:13,980] [INFO] Running command: hmmsearch --tblout GCF_007845645.1_ASM784564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e6fa8a0-4104-43f0-8eb8-07dc7acf661c/dqc_reference/reference_markers.hmm GCF_007845645.1_ASM784564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:14,360] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:14,362] [INFO] Found 6/6 markers.
[2024-01-24 13:23:14,411] [INFO] Query marker FASTA was written to GCF_007845645.1_ASM784564v1_genomic.fna/markers.fasta
[2024-01-24 13:23:14,412] [INFO] Task started: Blastn
[2024-01-24 13:23:14,412] [INFO] Running command: blastn -query GCF_007845645.1_ASM784564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e6fa8a0-4104-43f0-8eb8-07dc7acf661c/dqc_reference/reference_markers.fasta -out GCF_007845645.1_ASM784564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:15,568] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:15,572] [INFO] Selected 21 target genomes.
[2024-01-24 13:23:15,572] [INFO] Target genome list was writen to GCF_007845645.1_ASM784564v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:15,593] [INFO] Task started: fastANI
[2024-01-24 13:23:15,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg3628e744-6978-4eb9-9641-68e586610213/GCF_007845645.1_ASM784564v1_genomic.fna.gz --refList GCF_007845645.1_ASM784564v1_genomic.fna/target_genomes.txt --output GCF_007845645.1_ASM784564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:30,822] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:30,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e6fa8a0-4104-43f0-8eb8-07dc7acf661c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:30,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e6fa8a0-4104-43f0-8eb8-07dc7acf661c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:30,842] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:30,842] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:30,843] [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
Leekyejoonella antrihumi	strain=C5-26	GCA_007845645.1	1660198	1660198	type	True	100.0	1696	1703	95	conclusive
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	79.1664	492	1703	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	78.9995	470	1703	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	78.8565	514	1703	95	below_threshold
Flexivirga endophytica	strain=CGMCC 1.15085	GCA_014640635.1	1849103	1849103	type	True	78.69	479	1703	95	below_threshold
Flexivirga endophytica	strain=KCTC 39536	GCA_014652735.1	1849103	1849103	type	True	78.6899	482	1703	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	78.6175	486	1703	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	78.5862	491	1703	95	below_threshold
Luteipulveratus mongoliensis	strain=MN07-A0370	GCA_001190945.1	571913	571913	type	True	78.4812	442	1703	95	below_threshold
Branchiibius hedensis	strain=DSM 22951	GCA_003149195.1	672460	672460	type	True	78.3388	352	1703	95	below_threshold
Branchiibius hedensis	strain=DSM 22951	GCA_900108585.1	672460	672460	type	True	78.327	352	1703	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	77.939	299	1703	95	below_threshold
Ornithinimicrobium cavernae	strain=KCTC 49018	GCA_003121625.1	2666047	2666047	type	True	77.8932	304	1703	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.8383	281	1703	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	77.7674	297	1703	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	77.7443	280	1703	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	77.7387	278	1703	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	77.733	272	1703	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	77.6576	278	1703	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.6412	287	1703	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	77.6055	307	1703	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:30,844] [INFO] DFAST Taxonomy check result was written to GCF_007845645.1_ASM784564v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:30,845] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:30,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:30,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e6fa8a0-4104-43f0-8eb8-07dc7acf661c/dqc_reference/checkm_data
[2024-01-24 13:23:30,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:30,902] [INFO] Task started: CheckM
[2024-01-24 13:23:30,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007845645.1_ASM784564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007845645.1_ASM784564v1_genomic.fna/checkm_input GCF_007845645.1_ASM784564v1_genomic.fna/checkm_result
[2024-01-24 13:24:25,219] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:25,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:25,242] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:25,243] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:25,243] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007845645.1_ASM784564v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:25,243] [INFO] Task started: Blastn
[2024-01-24 13:24:25,244] [INFO] Running command: blastn -query GCF_007845645.1_ASM784564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e6fa8a0-4104-43f0-8eb8-07dc7acf661c/dqc_reference/reference_markers_gtdb.fasta -out GCF_007845645.1_ASM784564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:26,897] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:26,900] [INFO] Selected 20 target genomes.
[2024-01-24 13:24:26,900] [INFO] Target genome list was writen to GCF_007845645.1_ASM784564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:26,935] [INFO] Task started: fastANI
[2024-01-24 13:24:26,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg3628e744-6978-4eb9-9641-68e586610213/GCF_007845645.1_ASM784564v1_genomic.fna.gz --refList GCF_007845645.1_ASM784564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007845645.1_ASM784564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:42,164] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:42,183] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:42,184] [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_007845645.1	s__Leekyejoonella antrihumi	100.0	1696	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Leekyejoonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013002715.1	s__Flexivirga aerilata	79.1954	489	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001247745.1	s__Luteipulveratus halotolerans	78.9917	471	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190805.1	s__Flexivirga oryzae	78.8685	512	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410455.1	s__Allobranchiibius huperziae	78.7695	462	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius	95.0	97.04	97.04	0.91	0.91	2	-
GCF_014640635.1	s__Flexivirga endophytica	78.6988	478	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003386865.1	s__Yimella indica	78.66	416	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013135345.1	s__Yimella sp013135345	78.6498	452	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017565405.1	s__Allobranchiibius sp017565405	78.6133	463	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716095.1	s__Barrientosiimonas humi	78.5861	491	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Barrientosiimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001190945.1	s__Luteipulveratus mongoliensis	78.4813	442	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829035.1	s__Rudaeicoccus suwonensis	78.433	428	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Rudaeicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108585.1	s__Branchiibius hedensis	78.3388	351	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Branchiibius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111375.1	s__Pedococcus cremeus	78.1326	369	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_017654605.1	s__Yimella sp014530045	78.1264	358	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	98.79	97.58	0.96	0.92	3	-
GCF_900104525.1	s__Pedococcus dokdonensis	78.0945	362	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121625.1	s__Ornithinicoccus cavernae	77.8931	304	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636495.1	s__Ornithinimicrobium tianjinense	77.7563	279	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888335.1	s__Marihabitans sp016888335	77.7212	273	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429185.1	s__Terrabacter sp001429185	77.5695	361	1703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.06	99.06	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:42,185] [INFO] GTDB search result was written to GCF_007845645.1_ASM784564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:42,186] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:42,190] [INFO] DFAST_QC result json was written to GCF_007845645.1_ASM784564v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:42,190] [INFO] DFAST_QC completed!
[2024-01-24 13:24:42,191] [INFO] Total running time: 0h1m47s