[2024-01-24 14:22:15,297] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:15,299] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:15,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e6b4bb8-094d-46c1-ac9e-b9a9ba36dc8d/dqc_reference
[2024-01-24 14:22:16,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:16,627] [INFO] Task started: Prodigal
[2024-01-24 14:22:16,627] [INFO] Running command: gunzip -c /var/lib/cwl/stge5f0da34-4e3c-4aaf-9914-54a7dc81833b/GCF_006065315.1_ASM606531v1_genomic.fna.gz | prodigal -d GCF_006065315.1_ASM606531v1_genomic.fna/cds.fna -a GCF_006065315.1_ASM606531v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:34,150] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:34,150] [INFO] Task started: HMMsearch
[2024-01-24 14:22:34,150] [INFO] Running command: hmmsearch --tblout GCF_006065315.1_ASM606531v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e6b4bb8-094d-46c1-ac9e-b9a9ba36dc8d/dqc_reference/reference_markers.hmm GCF_006065315.1_ASM606531v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:34,435] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:34,436] [INFO] Found 6/6 markers.
[2024-01-24 14:22:34,479] [INFO] Query marker FASTA was written to GCF_006065315.1_ASM606531v1_genomic.fna/markers.fasta
[2024-01-24 14:22:34,479] [INFO] Task started: Blastn
[2024-01-24 14:22:34,479] [INFO] Running command: blastn -query GCF_006065315.1_ASM606531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e6b4bb8-094d-46c1-ac9e-b9a9ba36dc8d/dqc_reference/reference_markers.fasta -out GCF_006065315.1_ASM606531v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:35,168] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:35,171] [INFO] Selected 12 target genomes.
[2024-01-24 14:22:35,171] [INFO] Target genome list was writen to GCF_006065315.1_ASM606531v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:35,176] [INFO] Task started: fastANI
[2024-01-24 14:22:35,176] [INFO] Running command: fastANI --query /var/lib/cwl/stge5f0da34-4e3c-4aaf-9914-54a7dc81833b/GCF_006065315.1_ASM606531v1_genomic.fna.gz --refList GCF_006065315.1_ASM606531v1_genomic.fna/target_genomes.txt --output GCF_006065315.1_ASM606531v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:46,831] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:46,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e6b4bb8-094d-46c1-ac9e-b9a9ba36dc8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:46,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e6b4bb8-094d-46c1-ac9e-b9a9ba36dc8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:46,843] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:46,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:46,843] [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
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	100.0	1722	1722	95	conclusive
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	93.8597	1369	1722	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	92.3063	1284	1722	95	below_threshold
Aureibaculum marinum	strain=BH-SD17	GCA_003813905.1	2487930	2487930	type	True	80.0646	706	1722	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.0337	203	1722	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.9321	176	1722	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	76.8144	204	1722	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	76.6802	171	1722	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.6717	168	1722	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.6657	257	1722	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	76.6473	144	1722	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	76.3292	79	1722	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:46,845] [INFO] DFAST Taxonomy check result was written to GCF_006065315.1_ASM606531v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:46,846] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:46,847] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:46,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e6b4bb8-094d-46c1-ac9e-b9a9ba36dc8d/dqc_reference/checkm_data
[2024-01-24 14:22:46,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:46,898] [INFO] Task started: CheckM
[2024-01-24 14:22:46,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006065315.1_ASM606531v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006065315.1_ASM606531v1_genomic.fna/checkm_input GCF_006065315.1_ASM606531v1_genomic.fna/checkm_result
[2024-01-24 14:23:35,165] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:35,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:35,184] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:35,184] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:35,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006065315.1_ASM606531v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:35,185] [INFO] Task started: Blastn
[2024-01-24 14:23:35,185] [INFO] Running command: blastn -query GCF_006065315.1_ASM606531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e6b4bb8-094d-46c1-ac9e-b9a9ba36dc8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_006065315.1_ASM606531v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:36,041] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:36,045] [INFO] Selected 9 target genomes.
[2024-01-24 14:23:36,045] [INFO] Target genome list was writen to GCF_006065315.1_ASM606531v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:36,052] [INFO] Task started: fastANI
[2024-01-24 14:23:36,052] [INFO] Running command: fastANI --query /var/lib/cwl/stge5f0da34-4e3c-4aaf-9914-54a7dc81833b/GCF_006065315.1_ASM606531v1_genomic.fna.gz --refList GCF_006065315.1_ASM606531v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006065315.1_ASM606531v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:44,565] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:44,574] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:44,574] [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
GCA_006065315.1	s__Aureibaculum sp006065315	100.0	1721	1722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003449015.1	s__Aureibaculum sp003449015	93.8597	1369	1722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406085.1	s__Aureibaculum sp016406085	92.3289	1282	1722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813905.1	s__Aureibaculum marinum	80.0548	708	1722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352665.1	s__Aureibaculum sp002352665	77.8225	406	1722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260195.1	s__Lutibacter citreus	77.1929	258	1722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	77.0979	192	1722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	76.9181	171	1722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004195315.1	s__Lutibacter sp004195315	76.6163	136	1722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:44,575] [INFO] GTDB search result was written to GCF_006065315.1_ASM606531v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:44,576] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:44,579] [INFO] DFAST_QC result json was written to GCF_006065315.1_ASM606531v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:44,579] [INFO] DFAST_QC completed!
[2024-01-24 14:23:44,579] [INFO] Total running time: 0h1m29s