[2024-01-24 13:45:55,354] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:55,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:55,355] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc08c2f0-a7cb-4b73-9e4b-4029d70d79a4/dqc_reference
[2024-01-24 13:45:56,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:56,564] [INFO] Task started: Prodigal
[2024-01-24 13:45:56,565] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7dd6b8d-3eb0-4f83-8cd3-6591f03cbeef/GCF_014639075.1_ASM1463907v1_genomic.fna.gz | prodigal -d GCF_014639075.1_ASM1463907v1_genomic.fna/cds.fna -a GCF_014639075.1_ASM1463907v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:05,402] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:05,403] [INFO] Task started: HMMsearch
[2024-01-24 13:46:05,403] [INFO] Running command: hmmsearch --tblout GCF_014639075.1_ASM1463907v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc08c2f0-a7cb-4b73-9e4b-4029d70d79a4/dqc_reference/reference_markers.hmm GCF_014639075.1_ASM1463907v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:05,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:05,642] [INFO] Found 6/6 markers.
[2024-01-24 13:46:05,671] [INFO] Query marker FASTA was written to GCF_014639075.1_ASM1463907v1_genomic.fna/markers.fasta
[2024-01-24 13:46:05,671] [INFO] Task started: Blastn
[2024-01-24 13:46:05,671] [INFO] Running command: blastn -query GCF_014639075.1_ASM1463907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc08c2f0-a7cb-4b73-9e4b-4029d70d79a4/dqc_reference/reference_markers.fasta -out GCF_014639075.1_ASM1463907v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:06,490] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:06,493] [INFO] Selected 19 target genomes.
[2024-01-24 13:46:06,493] [INFO] Target genome list was writen to GCF_014639075.1_ASM1463907v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:06,522] [INFO] Task started: fastANI
[2024-01-24 13:46:06,522] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7dd6b8d-3eb0-4f83-8cd3-6591f03cbeef/GCF_014639075.1_ASM1463907v1_genomic.fna.gz --refList GCF_014639075.1_ASM1463907v1_genomic.fna/target_genomes.txt --output GCF_014639075.1_ASM1463907v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:18,784] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:18,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc08c2f0-a7cb-4b73-9e4b-4029d70d79a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:18,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc08c2f0-a7cb-4b73-9e4b-4029d70d79a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:18,805] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:18,805] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:18,805] [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
Glycocaulis albus	strain=CGMCC 1.12766	GCA_014639075.1	1382801	1382801	type	True	100.0	939	939	95	conclusive
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	86.5643	789	939	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	86.4887	799	939	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	78.1972	318	939	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	78.1399	326	939	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	78.0542	287	939	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	78.0047	287	939	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.8757	300	939	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	77.0613	53	939	95	below_threshold
Euryhalocaulis caribicus	strain=JL2009	GCA_000412185.1	1161401	1161401	type	True	77.0002	153	939	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.4874	95	939	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	76.2936	69	939	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	76.2741	67	939	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	76.0524	69	939	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	76.0307	67	939	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	75.9986	69	939	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	75.6811	90	939	95	below_threshold
Novosphingobium sediminicola	strain=DSM 27057	GCA_014196525.1	563162	563162	type	True	75.4809	71	939	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:18,807] [INFO] DFAST Taxonomy check result was written to GCF_014639075.1_ASM1463907v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:18,807] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:18,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:18,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc08c2f0-a7cb-4b73-9e4b-4029d70d79a4/dqc_reference/checkm_data
[2024-01-24 13:46:18,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:18,837] [INFO] Task started: CheckM
[2024-01-24 13:46:18,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014639075.1_ASM1463907v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014639075.1_ASM1463907v1_genomic.fna/checkm_input GCF_014639075.1_ASM1463907v1_genomic.fna/checkm_result
[2024-01-24 13:46:50,421] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:50,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:50,442] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:50,443] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:50,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014639075.1_ASM1463907v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:50,444] [INFO] Task started: Blastn
[2024-01-24 13:46:50,444] [INFO] Running command: blastn -query GCF_014639075.1_ASM1463907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc08c2f0-a7cb-4b73-9e4b-4029d70d79a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014639075.1_ASM1463907v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:51,923] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:51,927] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:51,927] [INFO] Target genome list was writen to GCF_014639075.1_ASM1463907v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:51,948] [INFO] Task started: fastANI
[2024-01-24 13:46:51,948] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7dd6b8d-3eb0-4f83-8cd3-6591f03cbeef/GCF_014639075.1_ASM1463907v1_genomic.fna.gz --refList GCF_014639075.1_ASM1463907v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014639075.1_ASM1463907v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:01,476] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:01,495] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:01,496] [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_014639075.1	s__Glycocaulis albus	100.0	939	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004000605.1	s__Glycocaulis alkaliphilus	86.4887	799	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000744995.1	s__Glycocaulis sp000744995	82.8635	714	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	98.48	98.48	0.95	0.95	2	-
GCF_007050995.1	s__Glycocaulis profundi	78.7688	368	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630495.1	s__Oceanicaulis satelles	78.4929	364	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	78.2203	324	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152745.1	s__Oceanicaulis sp000152745	78.1896	286	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_017161425.1	s__Marinicauda algicola	78.1004	327	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004793635.1	s__Marinicauda pacifica	78.0491	288	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000420265.1	s__Oceanicaulis alexandrii	77.8098	277	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	97.56	97.05	0.94	0.85	5	-
GCA_001510895.1	s__Mesorhizobium loti_A	76.4989	104	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127225.1	s__Sphingomonas sp002127225	76.0065	89	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761945.1	s__Sphingomonas leidyi	75.6811	90	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCA_017745215.1	s__Sphingomonas sp017745215	75.3604	64	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:01,497] [INFO] GTDB search result was written to GCF_014639075.1_ASM1463907v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:01,498] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:01,502] [INFO] DFAST_QC result json was written to GCF_014639075.1_ASM1463907v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:01,502] [INFO] DFAST_QC completed!
[2024-01-24 13:47:01,502] [INFO] Total running time: 0h1m6s