[2024-01-24 11:59:51,991] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:51,994] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:51,994] [INFO] DQC Reference Directory: /var/lib/cwl/stga42dd1c7-6fd1-473c-92fe-9707799aea34/dqc_reference
[2024-01-24 11:59:55,380] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:55,381] [INFO] Task started: Prodigal
[2024-01-24 11:59:55,382] [INFO] Running command: gunzip -c /var/lib/cwl/stg963f2b68-a9c6-4c89-a830-4f4dd7d37147/GCF_006716065.1_ASM671606v1_genomic.fna.gz | prodigal -d GCF_006716065.1_ASM671606v1_genomic.fna/cds.fna -a GCF_006716065.1_ASM671606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:13,837] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:13,838] [INFO] Task started: HMMsearch
[2024-01-24 12:00:13,838] [INFO] Running command: hmmsearch --tblout GCF_006716065.1_ASM671606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga42dd1c7-6fd1-473c-92fe-9707799aea34/dqc_reference/reference_markers.hmm GCF_006716065.1_ASM671606v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:14,135] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:14,136] [INFO] Found 6/6 markers.
[2024-01-24 12:00:14,191] [INFO] Query marker FASTA was written to GCF_006716065.1_ASM671606v1_genomic.fna/markers.fasta
[2024-01-24 12:00:14,191] [INFO] Task started: Blastn
[2024-01-24 12:00:14,192] [INFO] Running command: blastn -query GCF_006716065.1_ASM671606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga42dd1c7-6fd1-473c-92fe-9707799aea34/dqc_reference/reference_markers.fasta -out GCF_006716065.1_ASM671606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:15,301] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:15,306] [INFO] Selected 15 target genomes.
[2024-01-24 12:00:15,306] [INFO] Target genome list was writen to GCF_006716065.1_ASM671606v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:15,314] [INFO] Task started: fastANI
[2024-01-24 12:00:15,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg963f2b68-a9c6-4c89-a830-4f4dd7d37147/GCF_006716065.1_ASM671606v1_genomic.fna.gz --refList GCF_006716065.1_ASM671606v1_genomic.fna/target_genomes.txt --output GCF_006716065.1_ASM671606v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:34,942] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:34,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga42dd1c7-6fd1-473c-92fe-9707799aea34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:34,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga42dd1c7-6fd1-473c-92fe-9707799aea34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:34,955] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:34,956] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:34,956] [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
Salinispora arenicola	strain=DSM 44819	GCA_006716065.1	168697	168697	type	True	100.0	1876	1877	95	conclusive
Salinispora tropica	strain=CNB-440	GCA_000016425.1	168695	168695	type	True	87.9614	1333	1877	95	below_threshold
Salinispora pacifica	strain=CNR114	GCA_000514775.1	351187	351187	suspected-type	True	87.7271	1356	1877	95	below_threshold
Salinispora cortesiana	strain=CNY-202	GCA_000484695.1	1305843	1305843	type	True	87.601	1285	1877	95	below_threshold
Salinispora mooreana	strain=DSM 45549	GCA_000379065.1	999545	999545	type	True	87.5845	1279	1877	95	below_threshold
Salinispora mooreana	strain=CNT-150	GCA_000514435.1	999545	999545	type	True	87.5314	1254	1877	95	below_threshold
Salinispora fenicalii	strain=CNT-569	GCA_000514815.1	1137263	1137263	type	True	87.5231	1319	1877	95	below_threshold
Salinispora vitiensis	strain=CNT-148	GCA_000514675.1	999544	999544	type	True	87.2238	1224	1877	95	below_threshold
Salinispora vitiensis	strain=DSM 45548	GCA_000378825.1	999544	999544	type	True	87.2025	1232	1877	95	below_threshold
Salinispora oceanensis	strain=CNT-138	GCA_000514455.1	1050199	1050199	type	True	87.2015	1337	1877	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	82.5762	834	1877	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	81.8026	877	1877	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	81.5967	981	1877	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	81.5511	978	1877	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	81.4721	932	1877	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:34,958] [INFO] DFAST Taxonomy check result was written to GCF_006716065.1_ASM671606v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:34,958] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:34,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:34,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga42dd1c7-6fd1-473c-92fe-9707799aea34/dqc_reference/checkm_data
[2024-01-24 12:00:34,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:35,021] [INFO] Task started: CheckM
[2024-01-24 12:00:35,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716065.1_ASM671606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716065.1_ASM671606v1_genomic.fna/checkm_input GCF_006716065.1_ASM671606v1_genomic.fna/checkm_result
[2024-01-24 12:01:35,059] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:35,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:35,083] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:35,083] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:35,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716065.1_ASM671606v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:35,084] [INFO] Task started: Blastn
[2024-01-24 12:01:35,084] [INFO] Running command: blastn -query GCF_006716065.1_ASM671606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga42dd1c7-6fd1-473c-92fe-9707799aea34/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716065.1_ASM671606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:36,713] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:36,718] [INFO] Selected 9 target genomes.
[2024-01-24 12:01:36,718] [INFO] Target genome list was writen to GCF_006716065.1_ASM671606v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:36,727] [INFO] Task started: fastANI
[2024-01-24 12:01:36,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg963f2b68-a9c6-4c89-a830-4f4dd7d37147/GCF_006716065.1_ASM671606v1_genomic.fna.gz --refList GCF_006716065.1_ASM671606v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716065.1_ASM671606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:49,512] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:49,521] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:49,522] [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_006716065.1	s__Micromonospora arenicola	100.0	1876	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.41	96.39	0.90	0.85	49	conclusive
GCF_000016425.1	s__Micromonospora tropica	87.9794	1334	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.43	99.27	0.93	0.90	11	-
GCF_000514775.1	s__Micromonospora pacifica	87.7435	1355	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.56	96.63	0.90	0.86	17	-
GCF_000379065.1	s__Micromonospora mooreana	87.5969	1276	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.98	95.97	0.92	0.83	3	-
GCF_000484695.1	s__Micromonospora cortesiana	87.5773	1287	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000514815.1	s__Micromonospora fenicalii	87.4989	1322	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_000378825.1	s__Micromonospora vitiensis	87.2101	1229	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.04	95.56	0.89	0.83	4	-
GCF_000383575.1	s__Micromonospora oceanensis	87.2079	1349	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.54	95.98	0.89	0.84	12	-
GCF_004217535.1	s__Micromonospora sp004217535	84.7442	1089	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:49,523] [INFO] GTDB search result was written to GCF_006716065.1_ASM671606v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:49,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:49,528] [INFO] DFAST_QC result json was written to GCF_006716065.1_ASM671606v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:49,529] [INFO] DFAST_QC completed!
[2024-01-24 12:01:49,529] [INFO] Total running time: 0h1m58s