[2024-01-24 13:24:48,226] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:48,227] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:48,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a342f8e-0ce1-4359-a78a-bc19d7bb9100/dqc_reference
[2024-01-24 13:24:49,608] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:49,609] [INFO] Task started: Prodigal
[2024-01-24 13:24:49,609] [INFO] Running command: gunzip -c /var/lib/cwl/stg96758c78-7257-47ef-bc55-48ffbb17213e/GCF_000514455.1_ASM51445v1_genomic.fna.gz | prodigal -d GCF_000514455.1_ASM51445v1_genomic.fna/cds.fna -a GCF_000514455.1_ASM51445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:05,943] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:05,943] [INFO] Task started: HMMsearch
[2024-01-24 13:25:05,943] [INFO] Running command: hmmsearch --tblout GCF_000514455.1_ASM51445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a342f8e-0ce1-4359-a78a-bc19d7bb9100/dqc_reference/reference_markers.hmm GCF_000514455.1_ASM51445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:06,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:06,233] [INFO] Found 6/6 markers.
[2024-01-24 13:25:06,282] [INFO] Query marker FASTA was written to GCF_000514455.1_ASM51445v1_genomic.fna/markers.fasta
[2024-01-24 13:25:06,282] [INFO] Task started: Blastn
[2024-01-24 13:25:06,282] [INFO] Running command: blastn -query GCF_000514455.1_ASM51445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a342f8e-0ce1-4359-a78a-bc19d7bb9100/dqc_reference/reference_markers.fasta -out GCF_000514455.1_ASM51445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:07,454] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:07,458] [INFO] Selected 13 target genomes.
[2024-01-24 13:25:07,459] [INFO] Target genome list was writen to GCF_000514455.1_ASM51445v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:07,469] [INFO] Task started: fastANI
[2024-01-24 13:25:07,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg96758c78-7257-47ef-bc55-48ffbb17213e/GCF_000514455.1_ASM51445v1_genomic.fna.gz --refList GCF_000514455.1_ASM51445v1_genomic.fna/target_genomes.txt --output GCF_000514455.1_ASM51445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:24,802] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:24,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a342f8e-0ce1-4359-a78a-bc19d7bb9100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:24,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a342f8e-0ce1-4359-a78a-bc19d7bb9100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:24,814] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:25:24,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:24,814] [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 oceanensis	strain=CNT-138	GCA_000514455.1	1050199	1050199	type	True	100.0	1773	1775	95	conclusive
Salinispora oceanensis	strain=DSM 45547	GCA_000383575.1	1050199	1050199	type	True	99.9902	1774	1775	95	conclusive
Salinispora vitiensis	strain=CNT-148	GCA_000514675.1	999544	999544	type	True	93.3638	1422	1775	95	below_threshold
Salinispora vitiensis	strain=DSM 45548	GCA_000378825.1	999544	999544	type	True	93.3364	1446	1775	95	below_threshold
Salinispora pacifica	strain=CNR114	GCA_000514775.1	351187	351187	suspected-type	True	93.0579	1424	1775	95	below_threshold
Salinispora cortesiana	strain=CNY-202	GCA_000484695.1	1305843	1305843	type	True	92.9203	1356	1775	95	below_threshold
Salinispora mooreana	strain=DSM 45549	GCA_000379065.1	999545	999545	type	True	92.6759	1307	1775	95	below_threshold
Salinispora mooreana	strain=CNT-150	GCA_000514435.1	999545	999545	type	True	92.6742	1292	1775	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	82.5512	815	1775	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	81.6577	862	1775	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	81.5159	948	1775	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	81.4855	954	1775	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	81.4704	924	1775	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:24,815] [INFO] DFAST Taxonomy check result was written to GCF_000514455.1_ASM51445v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:24,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:24,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:24,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a342f8e-0ce1-4359-a78a-bc19d7bb9100/dqc_reference/checkm_data
[2024-01-24 13:25:24,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:24,867] [INFO] Task started: CheckM
[2024-01-24 13:25:24,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000514455.1_ASM51445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000514455.1_ASM51445v1_genomic.fna/checkm_input GCF_000514455.1_ASM51445v1_genomic.fna/checkm_result
[2024-01-24 13:26:12,855] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:12,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:12,877] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:12,877] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:12,878] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000514455.1_ASM51445v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:12,878] [INFO] Task started: Blastn
[2024-01-24 13:26:12,878] [INFO] Running command: blastn -query GCF_000514455.1_ASM51445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a342f8e-0ce1-4359-a78a-bc19d7bb9100/dqc_reference/reference_markers_gtdb.fasta -out GCF_000514455.1_ASM51445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:14,516] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:14,520] [INFO] Selected 6 target genomes.
[2024-01-24 13:26:14,520] [INFO] Target genome list was writen to GCF_000514455.1_ASM51445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:14,527] [INFO] Task started: fastANI
[2024-01-24 13:26:14,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg96758c78-7257-47ef-bc55-48ffbb17213e/GCF_000514455.1_ASM51445v1_genomic.fna.gz --refList GCF_000514455.1_ASM51445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000514455.1_ASM51445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:23,131] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:23,137] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:23,137] [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_000383575.1	s__Micromonospora oceanensis	99.9902	1774	1775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.54	95.98	0.89	0.84	12	conclusive
GCF_000378825.1	s__Micromonospora vitiensis	93.3364	1446	1775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.04	95.56	0.89	0.83	4	-
GCF_000514775.1	s__Micromonospora pacifica	93.0449	1425	1775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.56	96.63	0.90	0.86	17	-
GCF_000484695.1	s__Micromonospora cortesiana	92.907	1357	1775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379065.1	s__Micromonospora mooreana	92.6734	1307	1775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.98	95.97	0.92	0.83	3	-
GCF_000514815.1	s__Micromonospora fenicalii	91.9124	1377	1775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.96	98.96	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:23,139] [INFO] GTDB search result was written to GCF_000514455.1_ASM51445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:23,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:23,143] [INFO] DFAST_QC result json was written to GCF_000514455.1_ASM51445v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:23,143] [INFO] DFAST_QC completed!
[2024-01-24 13:26:23,144] [INFO] Total running time: 0h1m35s