[2024-01-24 14:05:49,082] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:49,084] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:49,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg95023d04-5299-490c-9c2d-1f6044458811/dqc_reference
[2024-01-24 14:05:50,368] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:50,369] [INFO] Task started: Prodigal
[2024-01-24 14:05:50,369] [INFO] Running command: gunzip -c /var/lib/cwl/stg07e08323-9ed8-49af-a715-24f40c43aab3/GCF_003402975.1_ASM340297v1_genomic.fna.gz | prodigal -d GCF_003402975.1_ASM340297v1_genomic.fna/cds.fna -a GCF_003402975.1_ASM340297v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:03,490] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:03,490] [INFO] Task started: HMMsearch
[2024-01-24 14:06:03,490] [INFO] Running command: hmmsearch --tblout GCF_003402975.1_ASM340297v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95023d04-5299-490c-9c2d-1f6044458811/dqc_reference/reference_markers.hmm GCF_003402975.1_ASM340297v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:03,804] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:03,806] [INFO] Found 6/6 markers.
[2024-01-24 14:06:03,870] [INFO] Query marker FASTA was written to GCF_003402975.1_ASM340297v1_genomic.fna/markers.fasta
[2024-01-24 14:06:03,871] [INFO] Task started: Blastn
[2024-01-24 14:06:03,871] [INFO] Running command: blastn -query GCF_003402975.1_ASM340297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95023d04-5299-490c-9c2d-1f6044458811/dqc_reference/reference_markers.fasta -out GCF_003402975.1_ASM340297v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:04,509] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:04,514] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:04,514] [INFO] Target genome list was writen to GCF_003402975.1_ASM340297v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:04,526] [INFO] Task started: fastANI
[2024-01-24 14:06:04,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg07e08323-9ed8-49af-a715-24f40c43aab3/GCF_003402975.1_ASM340297v1_genomic.fna.gz --refList GCF_003402975.1_ASM340297v1_genomic.fna/target_genomes.txt --output GCF_003402975.1_ASM340297v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:16,549] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:16,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95023d04-5299-490c-9c2d-1f6044458811/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:16,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95023d04-5299-490c-9c2d-1f6044458811/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:16,558] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:16,558] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:16,558] [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 aurantiacum	strain=N62	GCA_003402975.1	1737063	1737063	type	True	100.0	1128	1128	95	conclusive
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	79.8064	479	1128	95	below_threshold
Brumimicrobium glaciale	strain=IC156	GCA_004152935.1	200475	200475	type	True	79.2185	492	1128	95	below_threshold
Brumimicrobium salinarum	strain=LHR20	GCA_002844555.1	2058658	2058658	type	True	78.7297	323	1128	95	below_threshold
Lishizhenia tianjinensis	strain=CGMCC 1.7005	GCA_900116425.1	477690	477690	type	True	76.5464	88	1128	95	below_threshold
Crocinitomix catalasitica	strain=ATCC 23190	GCA_000621625.1	184607	184607	type	True	76.373	66	1128	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	75.2609	51	1128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:16,560] [INFO] DFAST Taxonomy check result was written to GCF_003402975.1_ASM340297v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:16,560] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:16,560] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:16,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95023d04-5299-490c-9c2d-1f6044458811/dqc_reference/checkm_data
[2024-01-24 14:06:16,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:16,597] [INFO] Task started: CheckM
[2024-01-24 14:06:16,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003402975.1_ASM340297v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003402975.1_ASM340297v1_genomic.fna/checkm_input GCF_003402975.1_ASM340297v1_genomic.fna/checkm_result
[2024-01-24 14:06:58,068] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:58,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:58,087] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:58,088] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:58,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003402975.1_ASM340297v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:58,089] [INFO] Task started: Blastn
[2024-01-24 14:06:58,089] [INFO] Running command: blastn -query GCF_003402975.1_ASM340297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95023d04-5299-490c-9c2d-1f6044458811/dqc_reference/reference_markers_gtdb.fasta -out GCF_003402975.1_ASM340297v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:58,897] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:58,941] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:58,942] [INFO] Target genome list was writen to GCF_003402975.1_ASM340297v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:58,961] [INFO] Task started: fastANI
[2024-01-24 14:06:58,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg07e08323-9ed8-49af-a715-24f40c43aab3/GCF_003402975.1_ASM340297v1_genomic.fna.gz --refList GCF_003402975.1_ASM340297v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003402975.1_ASM340297v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:06,633] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:06,648] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:06,649] [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_003402975.1	s__Brumimicrobium aurantiacum	100.0	1128	1128	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_003025005.1	s__Brumimicrobium mesophilum	79.8215	478	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152935.1	s__Brumimicrobium glaciale	79.2089	493	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143775.1	s__Brumimicrobium sp003143775	79.1063	475	1128	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	78.7435	322	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002734085.1	s__Brumimicrobium sp002734085	77.202	147	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117055.1	s__CSBr16-161 sp007117055	76.6013	56	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CSBr16-161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002331485.1	s__Brumimicrobium sp002331485	76.4179	128	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178305.1	s__CAIUKX01 sp016178305	76.0211	70	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002734065.2	s__UBA4466 sp002734065	75.9088	51	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:06,650] [INFO] GTDB search result was written to GCF_003402975.1_ASM340297v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:06,651] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:06,655] [INFO] DFAST_QC result json was written to GCF_003402975.1_ASM340297v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:06,655] [INFO] DFAST_QC completed!
[2024-01-24 14:07:06,655] [INFO] Total running time: 0h1m18s