[2024-01-24 14:06:44,630] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:44,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:44,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ef64b66-0ce1-4d46-8296-16d5f3b9cd99/dqc_reference
[2024-01-24 14:06:46,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:46,030] [INFO] Task started: Prodigal
[2024-01-24 14:06:46,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a1066c8-8e74-414c-bc37-55c064f8e047/GCF_004152865.1_ASM415286v1_genomic.fna.gz | prodigal -d GCF_004152865.1_ASM415286v1_genomic.fna/cds.fna -a GCF_004152865.1_ASM415286v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:59,315] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:59,315] [INFO] Task started: HMMsearch
[2024-01-24 14:06:59,315] [INFO] Running command: hmmsearch --tblout GCF_004152865.1_ASM415286v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ef64b66-0ce1-4d46-8296-16d5f3b9cd99/dqc_reference/reference_markers.hmm GCF_004152865.1_ASM415286v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:59,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:59,605] [INFO] Found 6/6 markers.
[2024-01-24 14:06:59,648] [INFO] Query marker FASTA was written to GCF_004152865.1_ASM415286v1_genomic.fna/markers.fasta
[2024-01-24 14:06:59,648] [INFO] Task started: Blastn
[2024-01-24 14:06:59,649] [INFO] Running command: blastn -query GCF_004152865.1_ASM415286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ef64b66-0ce1-4d46-8296-16d5f3b9cd99/dqc_reference/reference_markers.fasta -out GCF_004152865.1_ASM415286v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:00,590] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:00,595] [INFO] Selected 15 target genomes.
[2024-01-24 14:07:00,595] [INFO] Target genome list was writen to GCF_004152865.1_ASM415286v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:00,605] [INFO] Task started: fastANI
[2024-01-24 14:07:00,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a1066c8-8e74-414c-bc37-55c064f8e047/GCF_004152865.1_ASM415286v1_genomic.fna.gz --refList GCF_004152865.1_ASM415286v1_genomic.fna/target_genomes.txt --output GCF_004152865.1_ASM415286v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:14,835] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:14,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ef64b66-0ce1-4d46-8296-16d5f3b9cd99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:14,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ef64b66-0ce1-4d46-8296-16d5f3b9cd99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:14,852] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:14,852] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:14,852] [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 cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	100.0	1386	1389	95	conclusive
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	90.7272	1054	1389	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	86.5091	935	1389	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	84.35	875	1389	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	84.1929	868	1389	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	83.9646	864	1389	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	83.2843	736	1389	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	83.2388	759	1389	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	83.1752	789	1389	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	82.9951	767	1389	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	82.362	697	1389	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.133	340	1389	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.0632	360	1389	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.7644	340	1389	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.6008	388	1389	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:14,854] [INFO] DFAST Taxonomy check result was written to GCF_004152865.1_ASM415286v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:14,855] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:14,855] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:14,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ef64b66-0ce1-4d46-8296-16d5f3b9cd99/dqc_reference/checkm_data
[2024-01-24 14:07:14,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:14,904] [INFO] Task started: CheckM
[2024-01-24 14:07:14,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004152865.1_ASM415286v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004152865.1_ASM415286v1_genomic.fna/checkm_input GCF_004152865.1_ASM415286v1_genomic.fna/checkm_result
[2024-01-24 14:07:55,847] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:55,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:55,867] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:55,868] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:55,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004152865.1_ASM415286v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:55,868] [INFO] Task started: Blastn
[2024-01-24 14:07:55,869] [INFO] Running command: blastn -query GCF_004152865.1_ASM415286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ef64b66-0ce1-4d46-8296-16d5f3b9cd99/dqc_reference/reference_markers_gtdb.fasta -out GCF_004152865.1_ASM415286v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:57,738] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:57,741] [INFO] Selected 12 target genomes.
[2024-01-24 14:07:57,742] [INFO] Target genome list was writen to GCF_004152865.1_ASM415286v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:57,751] [INFO] Task started: fastANI
[2024-01-24 14:07:57,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a1066c8-8e74-414c-bc37-55c064f8e047/GCF_004152865.1_ASM415286v1_genomic.fna.gz --refList GCF_004152865.1_ASM415286v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004152865.1_ASM415286v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:10,571] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:10,585] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:10,586] [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_004152865.1	s__Sphingobium cupriresistens	100.0	1386	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	98.49	0.81	0.81	3	conclusive
GCA_013822485.1	s__Sphingobium sp013822485	90.8127	781	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927105.1	s__Sphingobium psychrophilum	90.7261	1055	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900013425.1	s__Sphingobium sp900013425	89.569	998	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.97	0.99	0.99	6	-
GCF_009720145.1	s__Sphingobium sp009720145	87.0505	946	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710155.1	s__Sphingobium limneticum	86.5063	935	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_001421665.1	s__Sphingobium sp001421665	86.3805	916	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203965.1	s__Sphingobium sp014203965	86.3455	908	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900109095.1	s__Sphingobium sp900109095	85.2135	901	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393185.1	s__Sphingobium lactosutens_A	84.9697	868	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508185.1	s__Sphingobium sp000508185	84.3692	802	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016000085.1	s__Sphingobium sp016000085	83.7777	696	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.94	98.94	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:10,588] [INFO] GTDB search result was written to GCF_004152865.1_ASM415286v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:10,589] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:10,592] [INFO] DFAST_QC result json was written to GCF_004152865.1_ASM415286v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:10,592] [INFO] DFAST_QC completed!
[2024-01-24 14:08:10,592] [INFO] Total running time: 0h1m26s