[2024-01-24 12:44:43,031] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,033] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,033] [INFO] DQC Reference Directory: /var/lib/cwl/stg0357dccd-0534-424c-96f1-99b3baaab99f/dqc_reference
[2024-01-24 12:44:44,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:44,482] [INFO] Task started: Prodigal
[2024-01-24 12:44:44,482] [INFO] Running command: gunzip -c /var/lib/cwl/stgce31a3fb-1b7a-4421-af37-0cd9baeb401a/GCF_015865035.1_ASM1586503v1_genomic.fna.gz | prodigal -d GCF_015865035.1_ASM1586503v1_genomic.fna/cds.fna -a GCF_015865035.1_ASM1586503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:57,509] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:57,510] [INFO] Task started: HMMsearch
[2024-01-24 12:44:57,510] [INFO] Running command: hmmsearch --tblout GCF_015865035.1_ASM1586503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0357dccd-0534-424c-96f1-99b3baaab99f/dqc_reference/reference_markers.hmm GCF_015865035.1_ASM1586503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:57,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:57,821] [INFO] Found 6/6 markers.
[2024-01-24 12:44:57,875] [INFO] Query marker FASTA was written to GCF_015865035.1_ASM1586503v1_genomic.fna/markers.fasta
[2024-01-24 12:44:57,876] [INFO] Task started: Blastn
[2024-01-24 12:44:57,876] [INFO] Running command: blastn -query GCF_015865035.1_ASM1586503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0357dccd-0534-424c-96f1-99b3baaab99f/dqc_reference/reference_markers.fasta -out GCF_015865035.1_ASM1586503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:58,965] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:58,970] [INFO] Selected 15 target genomes.
[2024-01-24 12:44:58,970] [INFO] Target genome list was writen to GCF_015865035.1_ASM1586503v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:58,980] [INFO] Task started: fastANI
[2024-01-24 12:44:58,981] [INFO] Running command: fastANI --query /var/lib/cwl/stgce31a3fb-1b7a-4421-af37-0cd9baeb401a/GCF_015865035.1_ASM1586503v1_genomic.fna.gz --refList GCF_015865035.1_ASM1586503v1_genomic.fna/target_genomes.txt --output GCF_015865035.1_ASM1586503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:14,703] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:14,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0357dccd-0534-424c-96f1-99b3baaab99f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:14,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0357dccd-0534-424c-96f1-99b3baaab99f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:14,716] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:14,716] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:14,717] [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 aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	100.0	1435	1436	95	conclusive
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	83.0704	855	1436	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	83.0434	870	1436	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	81.4221	626	1436	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	81.403	590	1436	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	81.0791	645	1436	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	80.7903	645	1436	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	80.7201	643	1436	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	80.6688	623	1436	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	80.6242	571	1436	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	80.4398	624	1436	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	79.9562	649	1436	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.5965	505	1436	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.3014	496	1436	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.7733	380	1436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:14,721] [INFO] DFAST Taxonomy check result was written to GCF_015865035.1_ASM1586503v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:14,721] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:14,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:14,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0357dccd-0534-424c-96f1-99b3baaab99f/dqc_reference/checkm_data
[2024-01-24 12:45:14,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:14,766] [INFO] Task started: CheckM
[2024-01-24 12:45:14,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015865035.1_ASM1586503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015865035.1_ASM1586503v1_genomic.fna/checkm_input GCF_015865035.1_ASM1586503v1_genomic.fna/checkm_result
[2024-01-24 12:45:54,164] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:54,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:54,187] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:54,187] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:54,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015865035.1_ASM1586503v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:54,188] [INFO] Task started: Blastn
[2024-01-24 12:45:54,188] [INFO] Running command: blastn -query GCF_015865035.1_ASM1586503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0357dccd-0534-424c-96f1-99b3baaab99f/dqc_reference/reference_markers_gtdb.fasta -out GCF_015865035.1_ASM1586503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:56,147] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:56,153] [INFO] Selected 16 target genomes.
[2024-01-24 12:45:56,153] [INFO] Target genome list was writen to GCF_015865035.1_ASM1586503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:56,179] [INFO] Task started: fastANI
[2024-01-24 12:45:56,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgce31a3fb-1b7a-4421-af37-0cd9baeb401a/GCF_015865035.1_ASM1586503v1_genomic.fna.gz --refList GCF_015865035.1_ASM1586503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015865035.1_ASM1586503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:12,837] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:12,851] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:12,851] [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_015865035.1	s__Novosphingobium sp015865035	100.0	1434	1436	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_018491765.1	s__Novosphingobium profundi	83.0572	857	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018417475.1	s__Novosphingobium sp000813185	83.0568	870	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCF_008107685.1	s__Novosphingobium sp008107685	82.2492	813	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590985.1	s__Novosphingobium naphthalenivorans	81.4134	628	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	81.3293	619	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	81.3029	698	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874585.1	s__Novosphingobium sp006874585	81.2726	749	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_001742225.1	s__Novosphingobium resinovorum	81.1643	733	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_900168325.1	s__Novosphingobium mathurense	81.1036	643	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.03	99.03	0.83	0.83	2	-
GCF_004341845.1	s__Novosphingobium sp004341845	80.8635	662	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645195.1	s__Novosphingobium indicum	80.7807	646	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	-
GCF_000802225.1	s__Novosphingobium malaysiense	80.7241	643	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342985.1	s__Novosphingobium sp004342985	80.6698	688	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.88	97.88	0.88	0.88	2	-
GCF_002149965.1	s__Novosphingobium panipatense	80.6165	699	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.24	97.74	0.85	0.82	3	-
GCF_902706195.1	s__Novosphingobium sp902706195	80.3503	662	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:12,854] [INFO] GTDB search result was written to GCF_015865035.1_ASM1586503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:12,854] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:12,859] [INFO] DFAST_QC result json was written to GCF_015865035.1_ASM1586503v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:12,859] [INFO] DFAST_QC completed!
[2024-01-24 12:46:12,859] [INFO] Total running time: 0h1m30s