[2024-01-25 18:44:05,663] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:05,666] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:05,666] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a0d5b77-40d0-4a78-8715-2ee5c5b53d96/dqc_reference
[2024-01-25 18:44:06,806] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:06,807] [INFO] Task started: Prodigal
[2024-01-25 18:44:06,807] [INFO] Running command: gunzip -c /var/lib/cwl/stg5869c575-ea11-468c-a82f-883ee10a15c8/GCF_000367345.1_ASM36734v1_genomic.fna.gz | prodigal -d GCF_000367345.1_ASM36734v1_genomic.fna/cds.fna -a GCF_000367345.1_ASM36734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:19,268] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:19,269] [INFO] Task started: HMMsearch
[2024-01-25 18:44:19,269] [INFO] Running command: hmmsearch --tblout GCF_000367345.1_ASM36734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a0d5b77-40d0-4a78-8715-2ee5c5b53d96/dqc_reference/reference_markers.hmm GCF_000367345.1_ASM36734v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:19,522] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:19,524] [INFO] Found 6/6 markers.
[2024-01-25 18:44:19,563] [INFO] Query marker FASTA was written to GCF_000367345.1_ASM36734v1_genomic.fna/markers.fasta
[2024-01-25 18:44:19,563] [INFO] Task started: Blastn
[2024-01-25 18:44:19,563] [INFO] Running command: blastn -query GCF_000367345.1_ASM36734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a0d5b77-40d0-4a78-8715-2ee5c5b53d96/dqc_reference/reference_markers.fasta -out GCF_000367345.1_ASM36734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:20,312] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:20,316] [INFO] Selected 12 target genomes.
[2024-01-25 18:44:20,317] [INFO] Target genome list was writen to GCF_000367345.1_ASM36734v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:20,321] [INFO] Task started: fastANI
[2024-01-25 18:44:20,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg5869c575-ea11-468c-a82f-883ee10a15c8/GCF_000367345.1_ASM36734v1_genomic.fna.gz --refList GCF_000367345.1_ASM36734v1_genomic.fna/target_genomes.txt --output GCF_000367345.1_ASM36734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:31,870] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:31,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a0d5b77-40d0-4a78-8715-2ee5c5b53d96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:31,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a0d5b77-40d0-4a78-8715-2ee5c5b53d96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:31,879] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:44:31,879] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:31,879] [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
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	100.0	1421	1426	95	conclusive
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	89.3075	896	1426	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	84.2107	856	1426	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	84.0343	859	1426	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	83.6191	805	1426	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	82.8143	769	1426	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	82.1956	704	1426	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	82.0472	700	1426	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	79.182	452	1426	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	78.0075	351	1426	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	77.787	320	1426	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.3068	273	1426	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:31,881] [INFO] DFAST Taxonomy check result was written to GCF_000367345.1_ASM36734v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:31,881] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:31,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:31,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a0d5b77-40d0-4a78-8715-2ee5c5b53d96/dqc_reference/checkm_data
[2024-01-25 18:44:31,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:31,924] [INFO] Task started: CheckM
[2024-01-25 18:44:31,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000367345.1_ASM36734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000367345.1_ASM36734v1_genomic.fna/checkm_input GCF_000367345.1_ASM36734v1_genomic.fna/checkm_result
[2024-01-25 18:45:10,239] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:10,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:10,257] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:10,258] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:10,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000367345.1_ASM36734v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:10,258] [INFO] Task started: Blastn
[2024-01-25 18:45:10,258] [INFO] Running command: blastn -query GCF_000367345.1_ASM36734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a0d5b77-40d0-4a78-8715-2ee5c5b53d96/dqc_reference/reference_markers_gtdb.fasta -out GCF_000367345.1_ASM36734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:11,543] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:11,546] [INFO] Selected 7 target genomes.
[2024-01-25 18:45:11,546] [INFO] Target genome list was writen to GCF_000367345.1_ASM36734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:11,552] [INFO] Task started: fastANI
[2024-01-25 18:45:11,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg5869c575-ea11-468c-a82f-883ee10a15c8/GCF_000367345.1_ASM36734v1_genomic.fna.gz --refList GCF_000367345.1_ASM36734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000367345.1_ASM36734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:18,662] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:18,667] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:18,668] [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_000367345.1	s__Sphingobium xenophagum	100.0	1421	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.29	96.67	0.79	0.71	22	conclusive
GCA_016463275.1	s__Sphingobium sp016463275	89.3226	641	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591655.1	s__Sphingobium sp003591655	89.3075	896	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019097845.1	s__Sphingobium sp019097845	89.0551	929	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382885.1	s__Sphingobium japonicum_C	88.8002	865	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280435.1	s__Sphingobium sp014280435	84.6081	816	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822485.1	s__Sphingobium sp013822485	84.1522	639	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:18,669] [INFO] GTDB search result was written to GCF_000367345.1_ASM36734v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:18,670] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:18,672] [INFO] DFAST_QC result json was written to GCF_000367345.1_ASM36734v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:18,673] [INFO] DFAST_QC completed!
[2024-01-25 18:45:18,673] [INFO] Total running time: 0h1m13s