[2024-01-24 13:58:40,825] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:40,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:40,830] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5b6c639-e292-4e4c-bcc6-b0753bd34210/dqc_reference
[2024-01-24 13:58:42,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:42,091] [INFO] Task started: Prodigal
[2024-01-24 13:58:42,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b5c44b6-e7ae-4abb-a1fe-ff44a01b9919/GCF_014652855.1_ASM1465285v1_genomic.fna.gz | prodigal -d GCF_014652855.1_ASM1465285v1_genomic.fna/cds.fna -a GCF_014652855.1_ASM1465285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:57,351] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:57,352] [INFO] Task started: HMMsearch
[2024-01-24 13:58:57,352] [INFO] Running command: hmmsearch --tblout GCF_014652855.1_ASM1465285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5b6c639-e292-4e4c-bcc6-b0753bd34210/dqc_reference/reference_markers.hmm GCF_014652855.1_ASM1465285v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:57,648] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:57,650] [INFO] Found 6/6 markers.
[2024-01-24 13:58:57,696] [INFO] Query marker FASTA was written to GCF_014652855.1_ASM1465285v1_genomic.fna/markers.fasta
[2024-01-24 13:58:57,697] [INFO] Task started: Blastn
[2024-01-24 13:58:57,697] [INFO] Running command: blastn -query GCF_014652855.1_ASM1465285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5b6c639-e292-4e4c-bcc6-b0753bd34210/dqc_reference/reference_markers.fasta -out GCF_014652855.1_ASM1465285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:58,714] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:58,717] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:58,718] [INFO] Target genome list was writen to GCF_014652855.1_ASM1465285v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:58,724] [INFO] Task started: fastANI
[2024-01-24 13:58:58,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b5c44b6-e7ae-4abb-a1fe-ff44a01b9919/GCF_014652855.1_ASM1465285v1_genomic.fna.gz --refList GCF_014652855.1_ASM1465285v1_genomic.fna/target_genomes.txt --output GCF_014652855.1_ASM1465285v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:14,107] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:14,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5b6c639-e292-4e4c-bcc6-b0753bd34210/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:14,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5b6c639-e292-4e4c-bcc6-b0753bd34210/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:14,124] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:14,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:14,125] [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 pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	100.0	1529	1529	95	conclusive
Novosphingobium capsulatum	strain=NBRC 12533	GCA_001598375.1	13688	13688	type	True	87.8831	1183	1529	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	81.1513	642	1529	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	80.8494	623	1529	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	80.7095	648	1529	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	80.3223	619	1529	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	80.2469	582	1529	95	below_threshold
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000375445.1	378548	378548	type	True	80.0432	569	1529	95	below_threshold
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000192575.1	378548	378548	type	True	80.021	568	1529	95	below_threshold
Novosphingobium taihuense	strain=CGMCC 1.3432	GCA_007830315.1	260085	260085	type	True	79.9436	583	1529	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	79.9046	591	1529	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	79.8835	574	1529	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	79.762	515	1529	95	below_threshold
Novosphingobium acidiphilum	strain=DSM 19966	GCA_000429005.1	505248	505248	type	True	79.3615	577	1529	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	78.7294	435	1529	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	78.4499	435	1529	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.3765	468	1529	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:14,126] [INFO] DFAST Taxonomy check result was written to GCF_014652855.1_ASM1465285v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:14,127] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:14,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:14,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5b6c639-e292-4e4c-bcc6-b0753bd34210/dqc_reference/checkm_data
[2024-01-24 13:59:14,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:14,178] [INFO] Task started: CheckM
[2024-01-24 13:59:14,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652855.1_ASM1465285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652855.1_ASM1465285v1_genomic.fna/checkm_input GCF_014652855.1_ASM1465285v1_genomic.fna/checkm_result
[2024-01-24 14:00:06,725] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:06,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:06,748] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:06,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:06,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652855.1_ASM1465285v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:06,749] [INFO] Task started: Blastn
[2024-01-24 14:00:06,749] [INFO] Running command: blastn -query GCF_014652855.1_ASM1465285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5b6c639-e292-4e4c-bcc6-b0753bd34210/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652855.1_ASM1465285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:08,580] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:08,584] [INFO] Selected 5 target genomes.
[2024-01-24 14:00:08,584] [INFO] Target genome list was writen to GCF_014652855.1_ASM1465285v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:08,594] [INFO] Task started: fastANI
[2024-01-24 14:00:08,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b5c44b6-e7ae-4abb-a1fe-ff44a01b9919/GCF_014652855.1_ASM1465285v1_genomic.fna.gz --refList GCF_014652855.1_ASM1465285v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652855.1_ASM1465285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:14,704] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:14,713] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:14,714] [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_014652855.1	s__Novosphingobium pokkalii	100.0	1529	1529	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_014200275.1	s__Novosphingobium sp014200275	88.0309	1056	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.74	98.09	0.91	0.86	7	-
GCF_001598375.1	s__Novosphingobium capsulatum	87.8906	1182	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.40	97.25	0.88	0.83	50	-
GCF_003208305.1	s__Novosphingobium sp003208305	86.3622	901	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015661825.1	s__Novosphingobium capsulatum_A	83.8925	687	1529	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 14:00:14,716] [INFO] GTDB search result was written to GCF_014652855.1_ASM1465285v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:14,717] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:14,721] [INFO] DFAST_QC result json was written to GCF_014652855.1_ASM1465285v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:14,721] [INFO] DFAST_QC completed!
[2024-01-24 14:00:14,722] [INFO] Total running time: 0h1m34s