[2024-01-24 10:57:26,819] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bdfc5d4-ee65-4de7-b555-e26552e80599/dqc_reference
[2024-01-24 10:57:28,255] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:28,255] [INFO] Task started: Prodigal
[2024-01-24 10:57:28,256] [INFO] Running command: gunzip -c /var/lib/cwl/stg57e7f0b4-05ed-4ff5-960c-d3a5bdb9c73c/GCF_016766835.1_ASM1676683v1_genomic.fna.gz | prodigal -d GCF_016766835.1_ASM1676683v1_genomic.fna/cds.fna -a GCF_016766835.1_ASM1676683v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:37,636] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:37,637] [INFO] Task started: HMMsearch
[2024-01-24 10:57:37,637] [INFO] Running command: hmmsearch --tblout GCF_016766835.1_ASM1676683v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bdfc5d4-ee65-4de7-b555-e26552e80599/dqc_reference/reference_markers.hmm GCF_016766835.1_ASM1676683v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:37,871] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:37,872] [INFO] Found 6/6 markers.
[2024-01-24 10:57:37,899] [INFO] Query marker FASTA was written to GCF_016766835.1_ASM1676683v1_genomic.fna/markers.fasta
[2024-01-24 10:57:37,899] [INFO] Task started: Blastn
[2024-01-24 10:57:37,899] [INFO] Running command: blastn -query GCF_016766835.1_ASM1676683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bdfc5d4-ee65-4de7-b555-e26552e80599/dqc_reference/reference_markers.fasta -out GCF_016766835.1_ASM1676683v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:39,148] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:39,151] [INFO] Selected 17 target genomes.
[2024-01-24 10:57:39,152] [INFO] Target genome list was writen to GCF_016766835.1_ASM1676683v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:39,158] [INFO] Task started: fastANI
[2024-01-24 10:57:39,159] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e7f0b4-05ed-4ff5-960c-d3a5bdb9c73c/GCF_016766835.1_ASM1676683v1_genomic.fna.gz --refList GCF_016766835.1_ASM1676683v1_genomic.fna/target_genomes.txt --output GCF_016766835.1_ASM1676683v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:51,244] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:51,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bdfc5d4-ee65-4de7-b555-e26552e80599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:51,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bdfc5d4-ee65-4de7-b555-e26552e80599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:51,258] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:51,259] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:51,259] [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
Dermacoccus nishinomiyaensis	strain=FDAARGOS_1119	GCA_016766835.1	1274	1274	type	True	100.0	1024	1024	95	conclusive
Dermacoccus nishinomiyaensis	strain=NCTC11039	GCA_900447535.1	1274	1274	type	True	99.9996	1014	1024	95	conclusive
Dermacoccus abyssi	strain=MT1.1	GCA_003515945.1	322596	322596	type	True	84.1263	679	1024	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	79.3068	425	1024	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	78.9354	406	1024	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	78.9353	407	1024	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	78.7754	333	1024	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.6619	314	1024	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	78.5701	370	1024	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	78.5339	384	1024	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.4761	326	1024	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.4094	266	1024	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.3614	314	1024	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.7695	242	1024	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	77.3044	276	1024	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.2132	305	1024	95	below_threshold
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	77.0866	253	1024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:51,264] [INFO] DFAST Taxonomy check result was written to GCF_016766835.1_ASM1676683v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:51,265] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:51,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:51,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bdfc5d4-ee65-4de7-b555-e26552e80599/dqc_reference/checkm_data
[2024-01-24 10:57:51,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:51,300] [INFO] Task started: CheckM
[2024-01-24 10:57:51,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016766835.1_ASM1676683v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016766835.1_ASM1676683v1_genomic.fna/checkm_input GCF_016766835.1_ASM1676683v1_genomic.fna/checkm_result
[2024-01-24 10:58:36,640] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:36,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:36,660] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:36,661] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:36,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016766835.1_ASM1676683v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:36,661] [INFO] Task started: Blastn
[2024-01-24 10:58:36,661] [INFO] Running command: blastn -query GCF_016766835.1_ASM1676683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bdfc5d4-ee65-4de7-b555-e26552e80599/dqc_reference/reference_markers_gtdb.fasta -out GCF_016766835.1_ASM1676683v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:38,534] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:38,541] [INFO] Selected 22 target genomes.
[2024-01-24 10:58:38,541] [INFO] Target genome list was writen to GCF_016766835.1_ASM1676683v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:38,555] [INFO] Task started: fastANI
[2024-01-24 10:58:38,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e7f0b4-05ed-4ff5-960c-d3a5bdb9c73c/GCF_016766835.1_ASM1676683v1_genomic.fna.gz --refList GCF_016766835.1_ASM1676683v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016766835.1_ASM1676683v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:56,658] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:56,675] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:56,675] [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_900447535.1	s__Dermacoccus nishinomiyaensis	99.9995	1015	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Dermacoccus	95.0	98.76	98.05	0.93	0.90	18	conclusive
GCF_003515945.1	s__Dermacoccus abyssi	84.0984	681	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Dermacoccus	95.0	97.58	97.20	0.89	0.88	6	-
GCF_001247745.1	s__Luteipulveratus halotolerans	79.3226	428	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.934	332	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716095.1	s__Barrientosiimonas humi	78.8944	409	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Barrientosiimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006715095.1	s__Yimella lutea	78.81	322	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	98.40	98.40	0.90	0.90	2	-
GCF_000768675.1	s__Knoellia flava	78.7945	332	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006715875.1	s__Terrabacter sp006715875	78.7724	362	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383675.1	s__Terrabacter sp000383675	78.7186	381	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297495.1	s__Janibacter hoylei	78.6427	323	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	99.95	99.95	0.99	0.99	2	-
GCF_900111375.1	s__Pedococcus cremeus	78.6022	359	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_000720925.1	s__Phycicoccus jejuensis	78.5874	380	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_007991735.1	s__Terrabacter aerolatus	78.5605	387	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428505.1	s__Terrabacter sp001428505	78.5475	395	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.23	99.23	0.97	0.97	2	-
GCF_013201035.1	s__Phycicoccus sp013201035	78.5304	401	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428025.1	s__Pedococcus sp001428025	78.5213	335	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620545.1	s__Terrabacter sp000620545	78.5036	341	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992835.1	s__Knoellia locipacati	78.4573	346	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104525.1	s__Pedococcus dokdonensis	78.4414	314	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956915.1	s__Monashia flava	78.3053	353	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Monashia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715055.1	s__Lapillicoccus jejuensis	78.1878	392	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428065.1	s__Phycicoccus sp001428065	78.1778	317	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:56,677] [INFO] GTDB search result was written to GCF_016766835.1_ASM1676683v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:56,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:56,681] [INFO] DFAST_QC result json was written to GCF_016766835.1_ASM1676683v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:56,681] [INFO] DFAST_QC completed!
[2024-01-24 10:58:56,682] [INFO] Total running time: 0h1m30s