[2024-01-25 20:03:05,677] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:05,680] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:05,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg27fed2bc-561c-4143-9827-9151d56ae3ca/dqc_reference
[2024-01-25 20:03:06,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:06,865] [INFO] Task started: Prodigal
[2024-01-25 20:03:06,865] [INFO] Running command: gunzip -c /var/lib/cwl/stga1d9b6b9-d6c3-4224-861b-7d8ee692e3a9/GCF_000445125.1_ASM44512v1_genomic.fna.gz | prodigal -d GCF_000445125.1_ASM44512v1_genomic.fna/cds.fna -a GCF_000445125.1_ASM44512v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:18,818] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:18,819] [INFO] Task started: HMMsearch
[2024-01-25 20:03:18,819] [INFO] Running command: hmmsearch --tblout GCF_000445125.1_ASM44512v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27fed2bc-561c-4143-9827-9151d56ae3ca/dqc_reference/reference_markers.hmm GCF_000445125.1_ASM44512v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:19,072] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:19,072] [INFO] Found 6/6 markers.
[2024-01-25 20:03:19,112] [INFO] Query marker FASTA was written to GCF_000445125.1_ASM44512v1_genomic.fna/markers.fasta
[2024-01-25 20:03:19,112] [INFO] Task started: Blastn
[2024-01-25 20:03:19,112] [INFO] Running command: blastn -query GCF_000445125.1_ASM44512v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27fed2bc-561c-4143-9827-9151d56ae3ca/dqc_reference/reference_markers.fasta -out GCF_000445125.1_ASM44512v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:20,016] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:20,019] [INFO] Selected 20 target genomes.
[2024-01-25 20:03:20,020] [INFO] Target genome list was writen to GCF_000445125.1_ASM44512v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:20,030] [INFO] Task started: fastANI
[2024-01-25 20:03:20,030] [INFO] Running command: fastANI --query /var/lib/cwl/stga1d9b6b9-d6c3-4224-861b-7d8ee692e3a9/GCF_000445125.1_ASM44512v1_genomic.fna.gz --refList GCF_000445125.1_ASM44512v1_genomic.fna/target_genomes.txt --output GCF_000445125.1_ASM44512v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:38,106] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:38,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27fed2bc-561c-4143-9827-9151d56ae3ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:38,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27fed2bc-561c-4143-9827-9151d56ae3ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:38,118] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:38,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:38,118] [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 lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	100.0	1537	1543	95	conclusive
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	81.763	728	1543	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	81.4483	599	1543	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	81.4117	673	1543	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	81.2518	569	1543	95	below_threshold
Novosphingobium barchaimii	strain=LL02	GCA_001046635.1	1420591	1420591	type	True	81.1756	700	1543	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	81.1701	592	1543	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	81.0393	596	1543	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	80.8957	587	1543	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	80.8848	624	1543	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	80.7184	608	1543	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	80.6975	539	1543	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	80.2347	507	1543	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	79.9986	416	1543	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.4922	459	1543	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.362	463	1543	95	below_threshold
Novosphingobium fluoreni	strain=DSM 27568	GCA_014196615.1	1391222	1391222	type	True	79.2897	442	1543	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	78.7215	377	1543	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	78.6784	381	1543	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.5091	348	1543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:38,120] [INFO] DFAST Taxonomy check result was written to GCF_000445125.1_ASM44512v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:38,120] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:38,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:38,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27fed2bc-561c-4143-9827-9151d56ae3ca/dqc_reference/checkm_data
[2024-01-25 20:03:38,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:38,167] [INFO] Task started: CheckM
[2024-01-25 20:03:38,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000445125.1_ASM44512v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000445125.1_ASM44512v1_genomic.fna/checkm_input GCF_000445125.1_ASM44512v1_genomic.fna/checkm_result
[2024-01-25 20:04:14,452] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:14,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:14,475] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:14,476] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:14,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000445125.1_ASM44512v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:14,477] [INFO] Task started: Blastn
[2024-01-25 20:04:14,477] [INFO] Running command: blastn -query GCF_000445125.1_ASM44512v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27fed2bc-561c-4143-9827-9151d56ae3ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_000445125.1_ASM44512v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:16,245] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:16,247] [INFO] Selected 9 target genomes.
[2024-01-25 20:04:16,247] [INFO] Target genome list was writen to GCF_000445125.1_ASM44512v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:16,257] [INFO] Task started: fastANI
[2024-01-25 20:04:16,257] [INFO] Running command: fastANI --query /var/lib/cwl/stga1d9b6b9-d6c3-4224-861b-7d8ee692e3a9/GCF_000445125.1_ASM44512v1_genomic.fna.gz --refList GCF_000445125.1_ASM44512v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000445125.1_ASM44512v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:26,967] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:26,974] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:26,974] [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_000445125.1	s__Novosphingobium lindaniclasticum	100.0	1537	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017745295.1	s__Novosphingobium sp017745295	86.5071	947	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	86.3464	985	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149965.1	s__Novosphingobium panipatense	86.1099	1040	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.24	97.74	0.85	0.82	3	-
GCF_004342985.1	s__Novosphingobium sp004342985	85.6971	1038	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.88	97.88	0.88	0.88	2	-
GCF_001298105.1	s__Novosphingobium sp001298105	84.4627	900	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.11	98.61	0.92	0.87	4	-
GCF_006874585.1	s__Novosphingobium sp006874585	83.7005	848	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_004341845.1	s__Novosphingobium sp004341845	83.1878	838	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706195.1	s__Novosphingobium sp902706195	81.1022	718	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:26,975] [INFO] GTDB search result was written to GCF_000445125.1_ASM44512v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:26,975] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:26,978] [INFO] DFAST_QC result json was written to GCF_000445125.1_ASM44512v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:26,978] [INFO] DFAST_QC completed!
[2024-01-25 20:04:26,979] [INFO] Total running time: 0h1m21s