[2024-01-24 14:11:46,594] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c8995b8-6562-4a3b-8c61-843d08a21ea2/dqc_reference
[2024-01-24 14:11:47,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:47,847] [INFO] Task started: Prodigal
[2024-01-24 14:11:47,847] [INFO] Running command: gunzip -c /var/lib/cwl/stgb86360c8-f1a8-4d75-aaff-acd68aa367cd/GCF_024171765.1_ASM2417176v1_genomic.fna.gz | prodigal -d GCF_024171765.1_ASM2417176v1_genomic.fna/cds.fna -a GCF_024171765.1_ASM2417176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:01,238] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:01,239] [INFO] Task started: HMMsearch
[2024-01-24 14:12:01,239] [INFO] Running command: hmmsearch --tblout GCF_024171765.1_ASM2417176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c8995b8-6562-4a3b-8c61-843d08a21ea2/dqc_reference/reference_markers.hmm GCF_024171765.1_ASM2417176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:01,501] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:01,503] [INFO] Found 6/6 markers.
[2024-01-24 14:12:01,547] [INFO] Query marker FASTA was written to GCF_024171765.1_ASM2417176v1_genomic.fna/markers.fasta
[2024-01-24 14:12:01,548] [INFO] Task started: Blastn
[2024-01-24 14:12:01,548] [INFO] Running command: blastn -query GCF_024171765.1_ASM2417176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c8995b8-6562-4a3b-8c61-843d08a21ea2/dqc_reference/reference_markers.fasta -out GCF_024171765.1_ASM2417176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:02,847] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:02,851] [INFO] Selected 10 target genomes.
[2024-01-24 14:12:02,852] [INFO] Target genome list was writen to GCF_024171765.1_ASM2417176v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:02,861] [INFO] Task started: fastANI
[2024-01-24 14:12:02,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgb86360c8-f1a8-4d75-aaff-acd68aa367cd/GCF_024171765.1_ASM2417176v1_genomic.fna.gz --refList GCF_024171765.1_ASM2417176v1_genomic.fna/target_genomes.txt --output GCF_024171765.1_ASM2417176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:13,267] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:13,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c8995b8-6562-4a3b-8c61-843d08a21ea2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:13,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c8995b8-6562-4a3b-8c61-843d08a21ea2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:13,278] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:13,278] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:13,278] [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
Williamsia deligens	strain=DSM 44902	GCA_024171765.1	321325	321325	type	True	100.0	1464	1466	95	conclusive
Williamsia serinedens	strain=DSM 45037	GCA_024171725.1	391736	391736	type	True	84.2935	1227	1466	95	below_threshold
Williamsia herbipolensis	strain=ARP1	GCA_000964005.1	1603258	1603258	type	True	81.2645	922	1466	95	below_threshold
Williamsia maris	strain=DSM 44693	GCA_024171815.1	72806	72806	type	True	80.7524	884	1466	95	below_threshold
Williamsia phyllosphaerae	strain=CCM 7855	GCA_014635305.1	885042	885042	type	True	80.4628	882	1466	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	79.4816	576	1466	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	79.1672	568	1466	95	below_threshold
Gordonia pseudamarae	strain=CON9	GCA_025273675.1	2831662	2831662	type	True	78.2578	488	1466	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	78.2231	448	1466	95	below_threshold
Dietzia lutea	strain=YIM 80766	GCA_003096075.1	546160	546160	type	True	77.8503	331	1466	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:13,280] [INFO] DFAST Taxonomy check result was written to GCF_024171765.1_ASM2417176v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:13,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:13,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:13,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c8995b8-6562-4a3b-8c61-843d08a21ea2/dqc_reference/checkm_data
[2024-01-24 14:12:13,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:13,324] [INFO] Task started: CheckM
[2024-01-24 14:12:13,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171765.1_ASM2417176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171765.1_ASM2417176v1_genomic.fna/checkm_input GCF_024171765.1_ASM2417176v1_genomic.fna/checkm_result
[2024-01-24 14:13:41,268] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:41,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:41,291] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:41,291] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:41,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171765.1_ASM2417176v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:41,292] [INFO] Task started: Blastn
[2024-01-24 14:13:41,292] [INFO] Running command: blastn -query GCF_024171765.1_ASM2417176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c8995b8-6562-4a3b-8c61-843d08a21ea2/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171765.1_ASM2417176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:43,256] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:43,260] [INFO] Selected 20 target genomes.
[2024-01-24 14:13:43,261] [INFO] Target genome list was writen to GCF_024171765.1_ASM2417176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:43,291] [INFO] Task started: fastANI
[2024-01-24 14:13:43,291] [INFO] Running command: fastANI --query /var/lib/cwl/stgb86360c8-f1a8-4d75-aaff-acd68aa367cd/GCF_024171765.1_ASM2417176v1_genomic.fna.gz --refList GCF_024171765.1_ASM2417176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171765.1_ASM2417176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:01,498] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:01,518] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:14:01,518] [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_000964005.1	s__Williamsia_A herbipolensis	81.2696	922	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	95.03	95.03	0.89	0.89	2	-
GCF_014635305.1	s__Williamsia_A phyllosphaerae	80.491	877	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462415.1	s__Williamsia_A sp016462415	80.4352	813	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344155.1	s__Gordonia paraffinivorans	79.4818	576	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_018474015.1	s__Williamsia_A sp018474015	79.2236	612	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298235.1	s__Gordonia namibiensis	79.151	571	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCA_014041935.1	s__Gordonia sp014041935	79.106	561	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.20	99.20	0.95	0.95	2	-
GCF_001485495.1	s__Gordonia desulfuricans	79.0465	550	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	-
GCF_000327325.1	s__Gordonia rubripertincta	79.0008	570	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_000332995.1	s__Gordonia amicalis	78.9365	559	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCA_013348785.1	s__Gordonia sp013348785	78.8892	470	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149015.1	s__Gordonia lacunae	78.8752	581	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855095.1	s__Gordonia insulae	78.713	586	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024785.1	s__Gordonia bronchialis	78.6937	547	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000241345.1	s__Gordonia amarae	78.6133	542	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.98	99.98	0.99	0.99	3	-
GCF_000738775.1	s__Rhodococcus defluvii	78.2364	447	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009914535.1	s__Gordonia pseudoamarae	78.2256	477	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.95	99.95	1.00	1.00	2	-
GCF_003051005.1	s__Rhodococcus sp003051005	78.0366	428	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096075.1	s__Dietzia lutea	77.8253	328	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000186325.1	s__Dietzia cinnamea_A	77.7192	300	1466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	96.59	96.10	0.87	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:01,520] [INFO] GTDB search result was written to GCF_024171765.1_ASM2417176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:01,522] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:01,527] [INFO] DFAST_QC result json was written to GCF_024171765.1_ASM2417176v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:01,528] [INFO] DFAST_QC completed!
[2024-01-24 14:14:01,528] [INFO] Total running time: 0h2m15s