[2024-01-25 18:16:35,463] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:35,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:35,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg0287411a-ae19-4c5e-8bdc-c534d91b65ad/dqc_reference
[2024-01-25 18:16:36,572] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:36,573] [INFO] Task started: Prodigal
[2024-01-25 18:16:36,573] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cb8ea0c-db18-48a7-9018-ddf6924521f7/GCF_003590145.2_ASM359014v2_genomic.fna.gz | prodigal -d GCF_003590145.2_ASM359014v2_genomic.fna/cds.fna -a GCF_003590145.2_ASM359014v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:47,410] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:47,410] [INFO] Task started: HMMsearch
[2024-01-25 18:16:47,410] [INFO] Running command: hmmsearch --tblout GCF_003590145.2_ASM359014v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0287411a-ae19-4c5e-8bdc-c534d91b65ad/dqc_reference/reference_markers.hmm GCF_003590145.2_ASM359014v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:47,623] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:47,624] [INFO] Found 6/6 markers.
[2024-01-25 18:16:47,656] [INFO] Query marker FASTA was written to GCF_003590145.2_ASM359014v2_genomic.fna/markers.fasta
[2024-01-25 18:16:47,656] [INFO] Task started: Blastn
[2024-01-25 18:16:47,656] [INFO] Running command: blastn -query GCF_003590145.2_ASM359014v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0287411a-ae19-4c5e-8bdc-c534d91b65ad/dqc_reference/reference_markers.fasta -out GCF_003590145.2_ASM359014v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:48,564] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:48,567] [INFO] Selected 18 target genomes.
[2024-01-25 18:16:48,567] [INFO] Target genome list was writen to GCF_003590145.2_ASM359014v2_genomic.fna/target_genomes.txt
[2024-01-25 18:16:48,587] [INFO] Task started: fastANI
[2024-01-25 18:16:48,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cb8ea0c-db18-48a7-9018-ddf6924521f7/GCF_003590145.2_ASM359014v2_genomic.fna.gz --refList GCF_003590145.2_ASM359014v2_genomic.fna/target_genomes.txt --output GCF_003590145.2_ASM359014v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:17:03,222] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:03,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0287411a-ae19-4c5e-8bdc-c534d91b65ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:17:03,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0287411a-ae19-4c5e-8bdc-c534d91b65ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:17:03,234] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:17:03,234] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:17:03,234] [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
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	100.0	1363	1364	95	conclusive
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	80.3747	673	1364	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	80.3347	664	1364	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	80.2682	681	1364	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	80.2423	677	1364	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	80.2351	682	1364	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	80.2039	674	1364	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	80.0619	674	1364	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	79.5744	528	1364	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	79.4669	536	1364	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0948	333	1364	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.0799	381	1364	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	77.9243	356	1364	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	77.6384	338	1364	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.5627	321	1364	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.5385	324	1364	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.489	289	1364	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	77.3295	249	1364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:17:03,240] [INFO] DFAST Taxonomy check result was written to GCF_003590145.2_ASM359014v2_genomic.fna/tc_result.tsv
[2024-01-25 18:17:03,241] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:17:03,241] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:17:03,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0287411a-ae19-4c5e-8bdc-c534d91b65ad/dqc_reference/checkm_data
[2024-01-25 18:17:03,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:17:03,286] [INFO] Task started: CheckM
[2024-01-25 18:17:03,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003590145.2_ASM359014v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003590145.2_ASM359014v2_genomic.fna/checkm_input GCF_003590145.2_ASM359014v2_genomic.fna/checkm_result
[2024-01-25 18:17:42,997] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:42,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:43,017] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:43,017] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:43,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003590145.2_ASM359014v2_genomic.fna/markers.fasta)
[2024-01-25 18:17:43,018] [INFO] Task started: Blastn
[2024-01-25 18:17:43,018] [INFO] Running command: blastn -query GCF_003590145.2_ASM359014v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0287411a-ae19-4c5e-8bdc-c534d91b65ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_003590145.2_ASM359014v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:44,761] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:44,764] [INFO] Selected 10 target genomes.
[2024-01-25 18:17:44,765] [INFO] Target genome list was writen to GCF_003590145.2_ASM359014v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:44,774] [INFO] Task started: fastANI
[2024-01-25 18:17:44,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cb8ea0c-db18-48a7-9018-ddf6924521f7/GCF_003590145.2_ASM359014v2_genomic.fna.gz --refList GCF_003590145.2_ASM359014v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003590145.2_ASM359014v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:53,756] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:53,762] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:53,763] [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_003590145.2	s__Pseudooceanicola algae	100.0	1362	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011806405.1	s__Pseudooceanicola sp011806405	82.1784	825	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	80.4054	676	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	80.3636	610	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	80.3171	666	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014899185.1	s__Pseudooceanicola antarcticus_A	80.2922	682	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	80.2511	674	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003575965.1	s__Pseudooceanicola sediminis	80.073	673	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.95	99.95	0.93	0.93	2	-
GCF_009857745.1	s__Thalassobius mangrovi	78.7366	507	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	78.3892	450	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:53,764] [INFO] GTDB search result was written to GCF_003590145.2_ASM359014v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:53,764] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:53,767] [INFO] DFAST_QC result json was written to GCF_003590145.2_ASM359014v2_genomic.fna/dqc_result.json
[2024-01-25 18:17:53,768] [INFO] DFAST_QC completed!
[2024-01-25 18:17:53,768] [INFO] Total running time: 0h1m18s