[2024-01-24 11:58:57,234] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,240] [INFO] DQC Reference Directory: /var/lib/cwl/stge2a5ca3f-7f43-49dd-939f-6783a4696f07/dqc_reference
[2024-01-24 11:58:58,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,583] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg89e483f3-2bc5-4953-94ad-fea52103056c/GCF_004152935.1_ASM415293v1_genomic.fna.gz | prodigal -d GCF_004152935.1_ASM415293v1_genomic.fna/cds.fna -a GCF_004152935.1_ASM415293v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:13,352] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:13,352] [INFO] Task started: HMMsearch
[2024-01-24 11:59:13,352] [INFO] Running command: hmmsearch --tblout GCF_004152935.1_ASM415293v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2a5ca3f-7f43-49dd-939f-6783a4696f07/dqc_reference/reference_markers.hmm GCF_004152935.1_ASM415293v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:13,660] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:13,661] [INFO] Found 6/6 markers.
[2024-01-24 11:59:13,714] [INFO] Query marker FASTA was written to GCF_004152935.1_ASM415293v1_genomic.fna/markers.fasta
[2024-01-24 11:59:13,714] [INFO] Task started: Blastn
[2024-01-24 11:59:13,715] [INFO] Running command: blastn -query GCF_004152935.1_ASM415293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2a5ca3f-7f43-49dd-939f-6783a4696f07/dqc_reference/reference_markers.fasta -out GCF_004152935.1_ASM415293v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:14,366] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:14,370] [INFO] Selected 16 target genomes.
[2024-01-24 11:59:14,370] [INFO] Target genome list was writen to GCF_004152935.1_ASM415293v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:14,377] [INFO] Task started: fastANI
[2024-01-24 11:59:14,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg89e483f3-2bc5-4953-94ad-fea52103056c/GCF_004152935.1_ASM415293v1_genomic.fna.gz --refList GCF_004152935.1_ASM415293v1_genomic.fna/target_genomes.txt --output GCF_004152935.1_ASM415293v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:26,977] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:26,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2a5ca3f-7f43-49dd-939f-6783a4696f07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:26,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2a5ca3f-7f43-49dd-939f-6783a4696f07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:26,985] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:26,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:26,986] [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
Brumimicrobium glaciale	strain=IC156	GCA_004152935.1	200475	200475	type	True	100.0	1416	1418	95	conclusive
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	80.6926	709	1418	95	below_threshold
Brumimicrobium aurantiacum	strain=N62	GCA_003402975.1	1737063	1737063	type	True	78.9118	501	1418	95	below_threshold
Brumimicrobium salinarum	strain=LHR20	GCA_002844555.1	2058658	2058658	type	True	78.0408	375	1418	95	below_threshold
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	76.647	75	1418	95	below_threshold
Lishizhenia tianjinensis	strain=CGMCC 1.7005	GCA_900116425.1	477690	477690	type	True	76.6381	74	1418	95	below_threshold
Crocinitomix catalasitica	strain=ATCC 23190	GCA_000621625.1	184607	184607	type	True	75.8164	59	1418	95	below_threshold
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	75.5517	72	1418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:26,991] [INFO] DFAST Taxonomy check result was written to GCF_004152935.1_ASM415293v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:26,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:26,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:26,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2a5ca3f-7f43-49dd-939f-6783a4696f07/dqc_reference/checkm_data
[2024-01-24 11:59:26,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:27,037] [INFO] Task started: CheckM
[2024-01-24 11:59:27,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004152935.1_ASM415293v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004152935.1_ASM415293v1_genomic.fna/checkm_input GCF_004152935.1_ASM415293v1_genomic.fna/checkm_result
[2024-01-24 12:00:12,478] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:12,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:12,494] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:12,494] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:12,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004152935.1_ASM415293v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:12,495] [INFO] Task started: Blastn
[2024-01-24 12:00:12,495] [INFO] Running command: blastn -query GCF_004152935.1_ASM415293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2a5ca3f-7f43-49dd-939f-6783a4696f07/dqc_reference/reference_markers_gtdb.fasta -out GCF_004152935.1_ASM415293v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:13,344] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:13,349] [INFO] Selected 12 target genomes.
[2024-01-24 12:00:13,350] [INFO] Target genome list was writen to GCF_004152935.1_ASM415293v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:13,360] [INFO] Task started: fastANI
[2024-01-24 12:00:13,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg89e483f3-2bc5-4953-94ad-fea52103056c/GCF_004152935.1_ASM415293v1_genomic.fna.gz --refList GCF_004152935.1_ASM415293v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004152935.1_ASM415293v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:21,664] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:21,673] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:21,673] [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_004152935.1	s__Brumimicrobium glaciale	100.0	1416	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003143775.1	s__Brumimicrobium sp003143775	80.8666	772	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025005.1	s__Brumimicrobium mesophilum	80.6786	711	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402975.1	s__Brumimicrobium aurantiacum	78.9298	499	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844555.1	s__Brumimicrobium salinarum	78.0395	374	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885545.1	s__M0103 sp009885545	76.2614	67	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984635.1	s__M0103 sp017984635	76.1568	73	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883325.1	s__UBA952 sp018883325	76.013	88	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767265.1	s__Aureivirga marina	75.54	73	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767245.1	s__Aureivirga sp015767245	75.3763	68	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:21,676] [INFO] GTDB search result was written to GCF_004152935.1_ASM415293v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:21,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:21,679] [INFO] DFAST_QC result json was written to GCF_004152935.1_ASM415293v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:21,679] [INFO] DFAST_QC completed!
[2024-01-24 12:00:21,680] [INFO] Total running time: 0h1m24s