[2023-06-27 07:23:08,770] [INFO] DFAST_QC pipeline started.
[2023-06-27 07:23:08,816] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 07:23:08,816] [INFO] DQC Reference Directory: /var/lib/cwl/stged840a3f-7a02-4e88-88f3-b8fc74ef13b8/dqc_reference
[2023-06-27 07:23:10,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 07:23:10,190] [INFO] Task started: Prodigal
[2023-06-27 07:23:10,190] [INFO] Running command: gunzip -c /var/lib/cwl/stg26274b60-21cf-4650-8023-2cc554e77558/GCA_026400375.1_ASM2640037v1_genomic.fna.gz | prodigal -d GCA_026400375.1_ASM2640037v1_genomic.fna/cds.fna -a GCA_026400375.1_ASM2640037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 07:23:20,967] [INFO] Task succeeded: Prodigal
[2023-06-27 07:23:20,967] [INFO] Task started: HMMsearch
[2023-06-27 07:23:20,967] [INFO] Running command: hmmsearch --tblout GCA_026400375.1_ASM2640037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged840a3f-7a02-4e88-88f3-b8fc74ef13b8/dqc_reference/reference_markers.hmm GCA_026400375.1_ASM2640037v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 07:23:21,259] [INFO] Task succeeded: HMMsearch
[2023-06-27 07:23:21,260] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg26274b60-21cf-4650-8023-2cc554e77558/GCA_026400375.1_ASM2640037v1_genomic.fna.gz]
[2023-06-27 07:23:21,294] [INFO] Query marker FASTA was written to GCA_026400375.1_ASM2640037v1_genomic.fna/markers.fasta
[2023-06-27 07:23:21,294] [INFO] Task started: Blastn
[2023-06-27 07:23:21,295] [INFO] Running command: blastn -query GCA_026400375.1_ASM2640037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged840a3f-7a02-4e88-88f3-b8fc74ef13b8/dqc_reference/reference_markers.fasta -out GCA_026400375.1_ASM2640037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:23:21,967] [INFO] Task succeeded: Blastn
[2023-06-27 07:23:21,978] [INFO] Selected 13 target genomes.
[2023-06-27 07:23:21,978] [INFO] Target genome list was writen to GCA_026400375.1_ASM2640037v1_genomic.fna/target_genomes.txt
[2023-06-27 07:23:21,987] [INFO] Task started: fastANI
[2023-06-27 07:23:21,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg26274b60-21cf-4650-8023-2cc554e77558/GCA_026400375.1_ASM2640037v1_genomic.fna.gz --refList GCA_026400375.1_ASM2640037v1_genomic.fna/target_genomes.txt --output GCA_026400375.1_ASM2640037v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 07:23:32,254] [INFO] Task succeeded: fastANI
[2023-06-27 07:23:32,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged840a3f-7a02-4e88-88f3-b8fc74ef13b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 07:23:32,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged840a3f-7a02-4e88-88f3-b8fc74ef13b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 07:23:32,266] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 07:23:32,266] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 07:23:32,266] [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 jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	82.8491	623	1053	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	82.6631	632	1053	95	below_threshold
Novosphingobium taihuense	strain=CGMCC 1.3432	GCA_007830315.1	260085	260085	type	True	82.611	634	1053	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	82.2823	625	1053	95	below_threshold
Novosphingobium subterraneum	strain=NBRC 16086	GCA_001598575.1	48936	48936	type	True	82.242	614	1053	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	81.8823	563	1053	95	below_threshold
Novosphingobium meiothermophilum	strain=SYSU G00007	GCA_003171715.1	2202251	2202251	type	True	81.6619	598	1053	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	80.7189	478	1053	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	80.4241	444	1053	95	below_threshold
Novosphingobium sediminis	strain=NBRC 106119	GCA_007991615.1	707214	707214	type	True	79.2772	423	1053	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	77.9405	245	1053	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.6086	213	1053	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.2403	206	1053	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 07:23:32,269] [INFO] DFAST Taxonomy check result was written to GCA_026400375.1_ASM2640037v1_genomic.fna/tc_result.tsv
[2023-06-27 07:23:32,269] [INFO] ===== Taxonomy check completed =====
[2023-06-27 07:23:32,270] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 07:23:32,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged840a3f-7a02-4e88-88f3-b8fc74ef13b8/dqc_reference/checkm_data
[2023-06-27 07:23:32,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 07:23:32,313] [INFO] Task started: CheckM
[2023-06-27 07:23:32,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026400375.1_ASM2640037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026400375.1_ASM2640037v1_genomic.fna/checkm_input GCA_026400375.1_ASM2640037v1_genomic.fna/checkm_result
[2023-06-27 07:24:07,757] [INFO] Task succeeded: CheckM
[2023-06-27 07:24:07,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 07:24:07,781] [INFO] ===== Completeness check finished =====
[2023-06-27 07:24:07,782] [INFO] ===== Start GTDB Search =====
[2023-06-27 07:24:07,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026400375.1_ASM2640037v1_genomic.fna/markers.fasta)
[2023-06-27 07:24:07,782] [INFO] Task started: Blastn
[2023-06-27 07:24:07,783] [INFO] Running command: blastn -query GCA_026400375.1_ASM2640037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged840a3f-7a02-4e88-88f3-b8fc74ef13b8/dqc_reference/reference_markers_gtdb.fasta -out GCA_026400375.1_ASM2640037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:24:08,700] [INFO] Task succeeded: Blastn
[2023-06-27 07:24:08,704] [INFO] Selected 12 target genomes.
[2023-06-27 07:24:08,704] [INFO] Target genome list was writen to GCA_026400375.1_ASM2640037v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 07:24:08,713] [INFO] Task started: fastANI
[2023-06-27 07:24:08,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg26274b60-21cf-4650-8023-2cc554e77558/GCA_026400375.1_ASM2640037v1_genomic.fna.gz --refList GCA_026400375.1_ASM2640037v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026400375.1_ASM2640037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 07:24:18,746] [INFO] Task succeeded: fastANI
[2023-06-27 07:24:18,763] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 07:24:18,764] [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
GCA_002256985.1	s__Novosphingobium sp002256985	85.4445	702	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.95	99.92	0.97	0.95	3	-
GCA_002256775.1	s__Novosphingobium sp002256775	83.6593	577	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641335.1	s__Novosphingobium sp012641335	83.2122	666	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694345.1	s__Novosphingobium jiangmenense	82.8534	622	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003454795.1	s__Novosphingobium sp003454795	82.6739	622	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.02	97.88	0.92	0.91	3	-
GCF_007830315.1	s__Novosphingobium taihuense	82.6239	633	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000807925.1	s__Novosphingobium subterraneum	82.2572	627	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.63	97.57	0.88	0.77	4	-
GCF_900176395.1	s__Novosphingobium sp900176395	81.927	565	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013325.1	s__Novosphingobium aromaticivorans	81.8731	564	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003171715.1	s__Novosphingobium meiothermophilum	81.6658	597	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117425.1	s__Novosphingobium sp900117425	79.703	435	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.26	96.76	0.88	0.87	3	-
GCF_007991615.1	s__Novosphingobium sediminis	79.2939	421	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 07:24:18,765] [INFO] GTDB search result was written to GCA_026400375.1_ASM2640037v1_genomic.fna/result_gtdb.tsv
[2023-06-27 07:24:18,766] [INFO] ===== GTDB Search completed =====
[2023-06-27 07:24:18,769] [INFO] DFAST_QC result json was written to GCA_026400375.1_ASM2640037v1_genomic.fna/dqc_result.json
[2023-06-27 07:24:18,770] [INFO] DFAST_QC completed!
[2023-06-27 07:24:18,770] [INFO] Total running time: 0h1m10s