[2023-06-30 08:35:03,314] [INFO] DFAST_QC pipeline started.
[2023-06-30 08:35:03,318] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 08:35:03,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg6072bf1a-8aba-40f1-9e9a-455827e11e6d/dqc_reference
[2023-06-30 08:35:04,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 08:35:04,678] [INFO] Task started: Prodigal
[2023-06-30 08:35:04,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d10b335-c19c-461c-aefd-d0657b0bb3a9/GCA_016710645.1_ASM1671064v1_genomic.fna.gz | prodigal -d GCA_016710645.1_ASM1671064v1_genomic.fna/cds.fna -a GCA_016710645.1_ASM1671064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 08:35:15,508] [INFO] Task succeeded: Prodigal
[2023-06-30 08:35:15,509] [INFO] Task started: HMMsearch
[2023-06-30 08:35:15,509] [INFO] Running command: hmmsearch --tblout GCA_016710645.1_ASM1671064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6072bf1a-8aba-40f1-9e9a-455827e11e6d/dqc_reference/reference_markers.hmm GCA_016710645.1_ASM1671064v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 08:35:15,802] [INFO] Task succeeded: HMMsearch
[2023-06-30 08:35:15,804] [INFO] Found 6/6 markers.
[2023-06-30 08:35:15,839] [INFO] Query marker FASTA was written to GCA_016710645.1_ASM1671064v1_genomic.fna/markers.fasta
[2023-06-30 08:35:15,840] [INFO] Task started: Blastn
[2023-06-30 08:35:15,840] [INFO] Running command: blastn -query GCA_016710645.1_ASM1671064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6072bf1a-8aba-40f1-9e9a-455827e11e6d/dqc_reference/reference_markers.fasta -out GCA_016710645.1_ASM1671064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:35:17,006] [INFO] Task succeeded: Blastn
[2023-06-30 08:35:17,011] [INFO] Selected 30 target genomes.
[2023-06-30 08:35:17,012] [INFO] Target genome list was writen to GCA_016710645.1_ASM1671064v1_genomic.fna/target_genomes.txt
[2023-06-30 08:35:17,063] [INFO] Task started: fastANI
[2023-06-30 08:35:17,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d10b335-c19c-461c-aefd-d0657b0bb3a9/GCA_016710645.1_ASM1671064v1_genomic.fna.gz --refList GCA_016710645.1_ASM1671064v1_genomic.fna/target_genomes.txt --output GCA_016710645.1_ASM1671064v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 08:35:37,029] [INFO] Task succeeded: fastANI
[2023-06-30 08:35:37,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6072bf1a-8aba-40f1-9e9a-455827e11e6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 08:35:37,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6072bf1a-8aba-40f1-9e9a-455827e11e6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 08:35:37,052] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 08:35:37,052] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 08:35:37,053] [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
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	78.8388	387	1127	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	78.7319	345	1127	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	78.6983	364	1127	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	78.6642	306	1127	95	below_threshold
Pedococcus badiiscoriae	strain=DSM 23987	GCA_013408925.1	642776	642776	type	True	78.6119	337	1127	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.5885	335	1127	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	78.5578	386	1127	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.5164	327	1127	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	78.4351	353	1127	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	78.4097	364	1127	95	below_threshold
Intrasporangium calvum	strain=DSM 43043	GCA_000184685.1	53358	53358	type	True	78.3768	338	1127	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	78.3505	308	1127	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	78.3494	329	1127	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	78.3401	309	1127	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	78.3259	326	1127	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.3095	336	1127	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	78.2552	268	1127	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	78.2079	279	1127	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	78.1957	302	1127	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	78.1306	315	1127	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	78.1281	265	1127	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	78.0513	279	1127	95	below_threshold
Ornithinimicrobium pekingense	strain=CGMCC 1.5362	GCA_014644955.1	384677	384677	type	True	78.0504	272	1127	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	78.0271	293	1127	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	78.0114	269	1127	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.9711	265	1127	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	77.6464	253	1127	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	77.3882	238	1127	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	76.8506	243	1127	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	76.7755	199	1127	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 08:35:37,055] [INFO] DFAST Taxonomy check result was written to GCA_016710645.1_ASM1671064v1_genomic.fna/tc_result.tsv
[2023-06-30 08:35:37,055] [INFO] ===== Taxonomy check completed =====
[2023-06-30 08:35:37,055] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 08:35:37,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6072bf1a-8aba-40f1-9e9a-455827e11e6d/dqc_reference/checkm_data
[2023-06-30 08:35:37,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 08:35:37,096] [INFO] Task started: CheckM
[2023-06-30 08:35:37,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016710645.1_ASM1671064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016710645.1_ASM1671064v1_genomic.fna/checkm_input GCA_016710645.1_ASM1671064v1_genomic.fna/checkm_result
[2023-06-30 08:36:14,293] [INFO] Task succeeded: CheckM
[2023-06-30 08:36:14,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 08:36:14,317] [INFO] ===== Completeness check finished =====
[2023-06-30 08:36:14,318] [INFO] ===== Start GTDB Search =====
[2023-06-30 08:36:14,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016710645.1_ASM1671064v1_genomic.fna/markers.fasta)
[2023-06-30 08:36:14,319] [INFO] Task started: Blastn
[2023-06-30 08:36:14,319] [INFO] Running command: blastn -query GCA_016710645.1_ASM1671064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6072bf1a-8aba-40f1-9e9a-455827e11e6d/dqc_reference/reference_markers_gtdb.fasta -out GCA_016710645.1_ASM1671064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:36:16,130] [INFO] Task succeeded: Blastn
[2023-06-30 08:36:16,135] [INFO] Selected 16 target genomes.
[2023-06-30 08:36:16,135] [INFO] Target genome list was writen to GCA_016710645.1_ASM1671064v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 08:36:16,170] [INFO] Task started: fastANI
[2023-06-30 08:36:16,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d10b335-c19c-461c-aefd-d0657b0bb3a9/GCA_016710645.1_ASM1671064v1_genomic.fna.gz --refList GCA_016710645.1_ASM1671064v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016710645.1_ASM1671064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 08:36:27,842] [INFO] Task succeeded: fastANI
[2023-06-30 08:36:27,859] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 08:36:27,860] [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_016710645.1	s__GCA-2748155 sp016710645	100.0	1120	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016710385.1	s__GCA-2748155 sp016710385	85.8843	844	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707175.1	s__GCA-2748155 sp016707175	80.5639	534	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	98.89	98.81	0.91	0.85	4	-
GCA_016715285.1	s__GCA-2748155 sp016715285	80.478	505	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	99.02	98.98	0.84	0.84	3	-
GCA_016704565.1	s__GCA-2748155 sp016704565	80.2539	554	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	97.96	97.36	0.89	0.86	3	-
GCA_016717165.1	s__JADKGA01 sp016717165	79.3017	385	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__JADKGA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748155.1	s__GCA-2748155 sp002748155	78.8834	204	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	78.8276	388	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_006715055.1	s__Lapillicoccus jejuensis	78.8045	418	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721155.3	s__Marihabitans melonis	78.4298	314	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	-
GCF_003635045.1	s__Terracoccus luteus	78.3942	387	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terracoccus	95.0	98.59	98.59	0.96	0.96	2	-
GCF_001426245.1	s__Pedococcus sp001426245	78.3868	343	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.80	98.80	0.95	0.95	2	-
GCF_006716095.1	s__Barrientosiimonas humi	78.2885	329	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Barrientosiimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013135345.1	s__Yimella sp013135345	78.1116	288	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000421185.1	s__Ornithinimicrobium pekingense	78.0802	275	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008919445.1	s__Serinicoccus sp008919445	77.7189	270	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 08:36:27,862] [INFO] GTDB search result was written to GCA_016710645.1_ASM1671064v1_genomic.fna/result_gtdb.tsv
[2023-06-30 08:36:27,862] [INFO] ===== GTDB Search completed =====
[2023-06-30 08:36:27,867] [INFO] DFAST_QC result json was written to GCA_016710645.1_ASM1671064v1_genomic.fna/dqc_result.json
[2023-06-30 08:36:27,867] [INFO] DFAST_QC completed!
[2023-06-30 08:36:27,867] [INFO] Total running time: 0h1m25s