[2024-01-24 13:31:57,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg986033fb-e98a-48ab-a5f6-dd32452e8a4b/dqc_reference
[2024-01-24 13:31:58,602] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,603] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,603] [INFO] Running command: gunzip -c /var/lib/cwl/stg811d411b-4278-4ae0-a0cc-bfa4f31978ce/GCF_007991615.1_ASM799161v1_genomic.fna.gz | prodigal -d GCF_007991615.1_ASM799161v1_genomic.fna/cds.fna -a GCF_007991615.1_ASM799161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:12,328] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:12,328] [INFO] Task started: HMMsearch
[2024-01-24 13:32:12,328] [INFO] Running command: hmmsearch --tblout GCF_007991615.1_ASM799161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg986033fb-e98a-48ab-a5f6-dd32452e8a4b/dqc_reference/reference_markers.hmm GCF_007991615.1_ASM799161v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:12,554] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:12,556] [INFO] Found 6/6 markers.
[2024-01-24 13:32:12,598] [INFO] Query marker FASTA was written to GCF_007991615.1_ASM799161v1_genomic.fna/markers.fasta
[2024-01-24 13:32:12,598] [INFO] Task started: Blastn
[2024-01-24 13:32:12,598] [INFO] Running command: blastn -query GCF_007991615.1_ASM799161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg986033fb-e98a-48ab-a5f6-dd32452e8a4b/dqc_reference/reference_markers.fasta -out GCF_007991615.1_ASM799161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:13,589] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:13,592] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:13,592] [INFO] Target genome list was writen to GCF_007991615.1_ASM799161v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:13,596] [INFO] Task started: fastANI
[2024-01-24 13:32:13,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg811d411b-4278-4ae0-a0cc-bfa4f31978ce/GCF_007991615.1_ASM799161v1_genomic.fna.gz --refList GCF_007991615.1_ASM799161v1_genomic.fna/target_genomes.txt --output GCF_007991615.1_ASM799161v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:26,266] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:26,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg986033fb-e98a-48ab-a5f6-dd32452e8a4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:26,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg986033fb-e98a-48ab-a5f6-dd32452e8a4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:26,279] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:26,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:26,280] [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
Novosphingobium sediminis	strain=NBRC 106119	GCA_007991615.1	707214	707214	type	True	100.0	1497	1498	95	conclusive
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	85.7675	966	1498	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	80.9876	634	1498	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	80.8654	661	1498	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	80.8506	612	1498	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	80.7813	632	1498	95	below_threshold
Novosphingobium subterraneum	strain=NBRC 16086	GCA_001598575.1	48936	48936	type	True	80.7653	608	1498	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	80.7582	648	1498	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	80.7241	595	1498	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	80.659	577	1498	95	below_threshold
Novosphingobium taihuense	strain=CGMCC 1.3432	GCA_007830315.1	260085	260085	type	True	80.6393	582	1498	95	below_threshold
Novosphingobium hassiacum	strain=DSM 14552	GCA_014196055.1	173676	173676	type	True	80.0672	554	1498	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	79.3839	471	1498	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.7196	371	1498	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.4712	342	1498	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.2572	351	1498	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:26,281] [INFO] DFAST Taxonomy check result was written to GCF_007991615.1_ASM799161v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:26,282] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:26,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:26,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg986033fb-e98a-48ab-a5f6-dd32452e8a4b/dqc_reference/checkm_data
[2024-01-24 13:32:26,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:26,325] [INFO] Task started: CheckM
[2024-01-24 13:32:26,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991615.1_ASM799161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991615.1_ASM799161v1_genomic.fna/checkm_input GCF_007991615.1_ASM799161v1_genomic.fna/checkm_result
[2024-01-24 13:33:09,930] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:09,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:09,962] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:09,963] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:09,963] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991615.1_ASM799161v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:09,963] [INFO] Task started: Blastn
[2024-01-24 13:33:09,964] [INFO] Running command: blastn -query GCF_007991615.1_ASM799161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg986033fb-e98a-48ab-a5f6-dd32452e8a4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991615.1_ASM799161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:11,887] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:11,890] [INFO] Selected 10 target genomes.
[2024-01-24 13:33:11,890] [INFO] Target genome list was writen to GCF_007991615.1_ASM799161v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:11,924] [INFO] Task started: fastANI
[2024-01-24 13:33:11,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg811d411b-4278-4ae0-a0cc-bfa4f31978ce/GCF_007991615.1_ASM799161v1_genomic.fna.gz --refList GCF_007991615.1_ASM799161v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991615.1_ASM799161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:21,804] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:21,814] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:21,814] [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_007991615.1	s__Novosphingobium sediminis	100.0	1497	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900117425.1	s__Novosphingobium sp900117425	87.33	1106	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.26	96.76	0.88	0.87	3	-
GCF_001519075.1	s__Novosphingobium fuchskuhlense	85.7638	966	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903834285.1	s__Novosphingobium sp903834285	85.3183	846	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.71	99.71	0.92	0.92	2	-
GCA_903828025.1	s__Novosphingobium sp903828025	82.4571	615	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927405.1	s__Novosphingobium olei	80.7684	647	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014975.1	s__Novosphingobium sp002336885	80.7551	638	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCF_000013325.1	s__Novosphingobium aromaticivorans	80.7349	594	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003454795.1	s__Novosphingobium sp003454795	80.7057	617	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.02	97.88	0.92	0.91	3	-
GCA_001725355.1	s__Novosphingobium sp001725355	80.5915	590	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:21,816] [INFO] GTDB search result was written to GCF_007991615.1_ASM799161v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:21,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:21,820] [INFO] DFAST_QC result json was written to GCF_007991615.1_ASM799161v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:21,821] [INFO] DFAST_QC completed!
[2024-01-24 13:33:21,821] [INFO] Total running time: 0h1m25s