[2024-01-24 14:39:15,642] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg658925d5-5611-4b68-b8ee-5db01b694f28/dqc_reference
[2024-01-24 14:39:18,586] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:18,589] [INFO] Task started: Prodigal
[2024-01-24 14:39:18,589] [INFO] Running command: gunzip -c /var/lib/cwl/stga2a6ff4c-8aa4-403a-9846-bb4b77f32bcc/GCF_000716095.1_ASM71609v1_genomic.fna.gz | prodigal -d GCF_000716095.1_ASM71609v1_genomic.fna/cds.fna -a GCF_000716095.1_ASM71609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:36,549] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:36,549] [INFO] Task started: HMMsearch
[2024-01-24 14:39:36,549] [INFO] Running command: hmmsearch --tblout GCF_000716095.1_ASM71609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg658925d5-5611-4b68-b8ee-5db01b694f28/dqc_reference/reference_markers.hmm GCF_000716095.1_ASM71609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:36,893] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:36,895] [INFO] Found 6/6 markers.
[2024-01-24 14:39:36,947] [INFO] Query marker FASTA was written to GCF_000716095.1_ASM71609v1_genomic.fna/markers.fasta
[2024-01-24 14:39:36,947] [INFO] Task started: Blastn
[2024-01-24 14:39:36,947] [INFO] Running command: blastn -query GCF_000716095.1_ASM71609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg658925d5-5611-4b68-b8ee-5db01b694f28/dqc_reference/reference_markers.fasta -out GCF_000716095.1_ASM71609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:38,254] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:38,257] [INFO] Selected 19 target genomes.
[2024-01-24 14:39:38,257] [INFO] Target genome list was writen to GCF_000716095.1_ASM71609v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:38,273] [INFO] Task started: fastANI
[2024-01-24 14:39:38,273] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a6ff4c-8aa4-403a-9846-bb4b77f32bcc/GCF_000716095.1_ASM71609v1_genomic.fna.gz --refList GCF_000716095.1_ASM71609v1_genomic.fna/target_genomes.txt --output GCF_000716095.1_ASM71609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:05,307] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:05,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg658925d5-5611-4b68-b8ee-5db01b694f28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:05,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg658925d5-5611-4b68-b8ee-5db01b694f28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:05,323] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:05,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:05,323] [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
Actinoalloteichus cyanogriseus	strain=DSM 43889	GCA_000429185.2	65497	65497	type	True	99.2768	1925	2051	95	conclusive
Actinoalloteichus spitiensis	strain=RMV-1378	GCA_000239155.2	252394	252394	type	True	92.3409	1303	2051	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	78.1542	694	2051	95	below_threshold
Actinoalloteichus hoggarensis	strain=DSM 45943	GCA_002234535.1	1470176	1470176	type	True	78.1498	742	2051	95	below_threshold
Actinoalloteichus hoggarensis	strain=CECT 8639	GCA_014203625.1	1470176	1470176	type	True	78.1188	743	2051	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	77.9727	723	2051	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	77.929	555	2051	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	77.9086	639	2051	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	77.7996	768	2051	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	77.7972	663	2051	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	77.7513	760	2051	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	77.554	545	2051	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	77.5259	598	2051	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	77.3957	759	2051	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	77.3922	708	2051	95	below_threshold
Crossiella equi	strain=NRRL B-24104	GCA_002155995.1	130796	130796	type	True	77.3631	711	2051	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	77.3173	614	2051	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	77.3106	574	2051	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	76.8248	699	2051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:05,325] [INFO] DFAST Taxonomy check result was written to GCF_000716095.1_ASM71609v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:05,326] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:05,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:05,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg658925d5-5611-4b68-b8ee-5db01b694f28/dqc_reference/checkm_data
[2024-01-24 14:40:05,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:05,403] [INFO] Task started: CheckM
[2024-01-24 14:40:05,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000716095.1_ASM71609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000716095.1_ASM71609v1_genomic.fna/checkm_input GCF_000716095.1_ASM71609v1_genomic.fna/checkm_result
[2024-01-24 14:40:59,072] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:59,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.49%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:59,097] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:59,097] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:59,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000716095.1_ASM71609v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:59,098] [INFO] Task started: Blastn
[2024-01-24 14:40:59,098] [INFO] Running command: blastn -query GCF_000716095.1_ASM71609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg658925d5-5611-4b68-b8ee-5db01b694f28/dqc_reference/reference_markers_gtdb.fasta -out GCF_000716095.1_ASM71609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:01,090] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:01,093] [INFO] Selected 16 target genomes.
[2024-01-24 14:41:01,093] [INFO] Target genome list was writen to GCF_000716095.1_ASM71609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:01,412] [INFO] Task started: fastANI
[2024-01-24 14:41:01,413] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a6ff4c-8aa4-403a-9846-bb4b77f32bcc/GCF_000716095.1_ASM71609v1_genomic.fna.gz --refList GCF_000716095.1_ASM71609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000716095.1_ASM71609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:24,254] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:24,273] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:24,273] [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_000429185.1	s__Actinoalloteichus cyanogriseus	99.2818	1903	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	99.50	99.47	0.98	0.97	3	conclusive
GCF_000239155.1	s__Actinoalloteichus spitiensis	92.3547	1302	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941625.1	s__Actinoalloteichus fjordicus	78.2215	762	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	99.71	99.71	0.98	0.98	2	-
GCF_002234535.1	s__Actinoalloteichus hoggarensis	78.1289	749	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	77.9605	725	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645795.1	s__Longimycelium tulufanense	77.9401	552	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Longimycelium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410345.1	s__Saccharopolyspora hordei	77.8996	640	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635025.1	s__Saccharopolyspora antimicrobica	77.7887	665	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	100.00	1.00	1.00	2	-
GCF_014648515.1	s__Actinosynnema coeruleofuscum	77.7505	757	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCA_000715825.1	s__Goodfellowiella coeruleoviolacea	77.6033	864	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758765.1	s__Amycolatopsis viridis	77.5307	549	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_014203355.1	s__Kutzneria kofuensis	77.4069	704	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876755.1	s__Crossiella equi	77.3806	756	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016907655.1	s__Actinosynnema algeriensis	77.3786	765	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262875.1	s__Amycolatopsis antarctica	77.2499	542	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	76.8563	561	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:24,276] [INFO] GTDB search result was written to GCF_000716095.1_ASM71609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:24,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:24,287] [INFO] DFAST_QC result json was written to GCF_000716095.1_ASM71609v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:24,288] [INFO] DFAST_QC completed!
[2024-01-24 14:41:24,288] [INFO] Total running time: 0h2m9s