[2024-01-24 15:11:03,117] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:11:03,119] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:11:03,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg5aebf745-1501-4070-8b4d-8ebb027a7122/dqc_reference
[2024-01-24 15:11:04,391] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:11:04,392] [INFO] Task started: Prodigal
[2024-01-24 15:11:04,392] [INFO] Running command: gunzip -c /var/lib/cwl/stg6313b496-2d04-4b17-867c-934ef1daa287/GCF_000429005.1_ASM42900v1_genomic.fna.gz | prodigal -d GCF_000429005.1_ASM42900v1_genomic.fna/cds.fna -a GCF_000429005.1_ASM42900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:18,616] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:18,617] [INFO] Task started: HMMsearch
[2024-01-24 15:11:18,617] [INFO] Running command: hmmsearch --tblout GCF_000429005.1_ASM42900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5aebf745-1501-4070-8b4d-8ebb027a7122/dqc_reference/reference_markers.hmm GCF_000429005.1_ASM42900v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:18,873] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:18,874] [INFO] Found 6/6 markers.
[2024-01-24 15:11:18,908] [INFO] Query marker FASTA was written to GCF_000429005.1_ASM42900v1_genomic.fna/markers.fasta
[2024-01-24 15:11:18,909] [INFO] Task started: Blastn
[2024-01-24 15:11:18,909] [INFO] Running command: blastn -query GCF_000429005.1_ASM42900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5aebf745-1501-4070-8b4d-8ebb027a7122/dqc_reference/reference_markers.fasta -out GCF_000429005.1_ASM42900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:19,918] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:19,921] [INFO] Selected 16 target genomes.
[2024-01-24 15:11:19,922] [INFO] Target genome list was writen to GCF_000429005.1_ASM42900v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:19,942] [INFO] Task started: fastANI
[2024-01-24 15:11:19,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg6313b496-2d04-4b17-867c-934ef1daa287/GCF_000429005.1_ASM42900v1_genomic.fna.gz --refList GCF_000429005.1_ASM42900v1_genomic.fna/target_genomes.txt --output GCF_000429005.1_ASM42900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:33,462] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:33,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5aebf745-1501-4070-8b4d-8ebb027a7122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:33,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5aebf745-1501-4070-8b4d-8ebb027a7122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:33,476] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:33,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:33,476] [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 acidiphilum	strain=DSM 19966	GCA_000429005.1	505248	505248	type	True	100.0	1210	1212	95	conclusive
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000375445.1	378548	378548	type	True	79.4657	569	1212	95	below_threshold
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000192575.1	378548	378548	type	True	79.4444	570	1212	95	below_threshold
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	79.3829	575	1212	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	79.2978	473	1212	95	below_threshold
Novosphingobium capsulatum	strain=NBRC 12533	GCA_001598375.1	13688	13688	type	True	79.2502	573	1212	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	79.0544	471	1212	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.0294	530	1212	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.8792	464	1212	95	below_threshold
Novosphingobium hassiacum	strain=DSM 14552	GCA_014196055.1	173676	173676	type	True	78.5199	421	1212	95	below_threshold
Novosphingobium meiothermophilum	strain=SYSU G00007	GCA_003171715.1	2202251	2202251	type	True	78.4025	406	1212	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	78.309	414	1212	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	78.1948	386	1212	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.7956	324	1212	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.7025	251	1212	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	77.1428	272	1212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:33,478] [INFO] DFAST Taxonomy check result was written to GCF_000429005.1_ASM42900v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:33,478] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:33,479] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:33,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5aebf745-1501-4070-8b4d-8ebb027a7122/dqc_reference/checkm_data
[2024-01-24 15:11:33,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:33,518] [INFO] Task started: CheckM
[2024-01-24 15:11:33,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429005.1_ASM42900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429005.1_ASM42900v1_genomic.fna/checkm_input GCF_000429005.1_ASM42900v1_genomic.fna/checkm_result
[2024-01-24 15:12:23,253] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:23,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:23,277] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:23,277] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:23,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429005.1_ASM42900v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:23,278] [INFO] Task started: Blastn
[2024-01-24 15:12:23,278] [INFO] Running command: blastn -query GCF_000429005.1_ASM42900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5aebf745-1501-4070-8b4d-8ebb027a7122/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429005.1_ASM42900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:24,943] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:24,946] [INFO] Selected 10 target genomes.
[2024-01-24 15:12:24,947] [INFO] Target genome list was writen to GCF_000429005.1_ASM42900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:24,956] [INFO] Task started: fastANI
[2024-01-24 15:12:24,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg6313b496-2d04-4b17-867c-934ef1daa287/GCF_000429005.1_ASM42900v1_genomic.fna.gz --refList GCF_000429005.1_ASM42900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429005.1_ASM42900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:33,566] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:33,577] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:33,578] [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_000429005.1	s__Novosphingobium acidiphilum	100.0	1210	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.82	98.58	0.89	0.82	13	conclusive
GCF_001519065.1	s__Novosphingobium sp001519065	84.1276	914	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832325.1	s__Novosphingobium sp903832325	83.3656	890	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.98	99.94	0.97	0.96	4	-
GCF_001519055.1	s__Novosphingobium sp001519055	82.1202	805	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893935.1	s__Novosphingobium sp903893935	81.4406	443	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868655.1	s__Novosphingobium sp903868655	81.4334	473	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848655.1	s__Novosphingobium sp903848655	80.6356	575	1212	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	79.3983	519	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCA_001725355.1	s__Novosphingobium sp001725355	79.2117	485	1212	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	78.3281	413	1212	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 15:12:33,579] [INFO] GTDB search result was written to GCF_000429005.1_ASM42900v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:33,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:33,583] [INFO] DFAST_QC result json was written to GCF_000429005.1_ASM42900v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:33,583] [INFO] DFAST_QC completed!
[2024-01-24 15:12:33,584] [INFO] Total running time: 0h1m30s