[2024-01-25 19:35:51,166] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:51,169] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:51,169] [INFO] DQC Reference Directory: /var/lib/cwl/stga76f567b-fd94-4ae5-9ee8-a3d3f61ddef2/dqc_reference
[2024-01-25 19:35:52,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:52,387] [INFO] Task started: Prodigal
[2024-01-25 19:35:52,388] [INFO] Running command: gunzip -c /var/lib/cwl/stgde03027a-50dc-46ea-aec8-830ae400c8b6/GCF_022832385.1_ASM2283238v1_genomic.fna.gz | prodigal -d GCF_022832385.1_ASM2283238v1_genomic.fna/cds.fna -a GCF_022832385.1_ASM2283238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:04,448] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:04,448] [INFO] Task started: HMMsearch
[2024-01-25 19:36:04,449] [INFO] Running command: hmmsearch --tblout GCF_022832385.1_ASM2283238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga76f567b-fd94-4ae5-9ee8-a3d3f61ddef2/dqc_reference/reference_markers.hmm GCF_022832385.1_ASM2283238v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:04,720] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:04,721] [INFO] Found 6/6 markers.
[2024-01-25 19:36:04,759] [INFO] Query marker FASTA was written to GCF_022832385.1_ASM2283238v1_genomic.fna/markers.fasta
[2024-01-25 19:36:04,760] [INFO] Task started: Blastn
[2024-01-25 19:36:04,760] [INFO] Running command: blastn -query GCF_022832385.1_ASM2283238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga76f567b-fd94-4ae5-9ee8-a3d3f61ddef2/dqc_reference/reference_markers.fasta -out GCF_022832385.1_ASM2283238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:05,697] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:05,701] [INFO] Selected 15 target genomes.
[2024-01-25 19:36:05,701] [INFO] Target genome list was writen to GCF_022832385.1_ASM2283238v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:05,708] [INFO] Task started: fastANI
[2024-01-25 19:36:05,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgde03027a-50dc-46ea-aec8-830ae400c8b6/GCF_022832385.1_ASM2283238v1_genomic.fna.gz --refList GCF_022832385.1_ASM2283238v1_genomic.fna/target_genomes.txt --output GCF_022832385.1_ASM2283238v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:21,325] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:21,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga76f567b-fd94-4ae5-9ee8-a3d3f61ddef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:21,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga76f567b-fd94-4ae5-9ee8-a3d3f61ddef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:21,338] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:36:21,338] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:36:21,338] [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 naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	87.2743	900	1448	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	83.2793	913	1448	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	82.8361	883	1448	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	81.5628	621	1448	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	81.5579	639	1448	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	81.5133	646	1448	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	81.2943	652	1448	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	80.7962	647	1448	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	80.7573	639	1448	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	80.6368	605	1448	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	80.6352	639	1448	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	80.3793	597	1448	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.6731	486	1448	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.665	469	1448	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.2598	488	1448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:21,341] [INFO] DFAST Taxonomy check result was written to GCF_022832385.1_ASM2283238v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:21,342] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:21,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:21,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga76f567b-fd94-4ae5-9ee8-a3d3f61ddef2/dqc_reference/checkm_data
[2024-01-25 19:36:21,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:21,389] [INFO] Task started: CheckM
[2024-01-25 19:36:21,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022832385.1_ASM2283238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022832385.1_ASM2283238v1_genomic.fna/checkm_input GCF_022832385.1_ASM2283238v1_genomic.fna/checkm_result
[2024-01-25 19:36:58,470] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:58,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:58,493] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:58,493] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:58,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022832385.1_ASM2283238v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:58,494] [INFO] Task started: Blastn
[2024-01-25 19:36:58,494] [INFO] Running command: blastn -query GCF_022832385.1_ASM2283238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga76f567b-fd94-4ae5-9ee8-a3d3f61ddef2/dqc_reference/reference_markers_gtdb.fasta -out GCF_022832385.1_ASM2283238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:00,316] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:00,319] [INFO] Selected 16 target genomes.
[2024-01-25 19:37:00,319] [INFO] Target genome list was writen to GCF_022832385.1_ASM2283238v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:00,352] [INFO] Task started: fastANI
[2024-01-25 19:37:00,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgde03027a-50dc-46ea-aec8-830ae400c8b6/GCF_022832385.1_ASM2283238v1_genomic.fna.gz --refList GCF_022832385.1_ASM2283238v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022832385.1_ASM2283238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:16,731] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:16,741] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:37:16,741] [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_001590985.1	s__Novosphingobium naphthalenivorans	87.2743	900	1448	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	83.2793	913	1448	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	82.8176	885	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113255.1	s__Novosphingobium sp900113255	81.8439	686	1448	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	81.5601	638	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_006874585.1	s__Novosphingobium sp006874585	81.5474	695	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_000281975.1	s__Novosphingobium sp000281975	81.4883	708	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168325.1	s__Novosphingobium mathurense	81.4845	650	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.03	99.03	0.83	0.83	2	-
GCF_014640675.1	s__Novosphingobium endophyticum	81.3113	650	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	81.226	679	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745295.1	s__Novosphingobium sp017745295	81.218	605	1448	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	80.9775	677	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.88	97.88	0.88	0.88	2	-
GCF_015865035.1	s__Novosphingobium sp015865035	80.7831	647	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298105.1	s__Novosphingobium sp001298105	80.746	698	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.11	98.61	0.92	0.87	4	-
GCF_018417475.1	s__Novosphingobium sp000813185	80.6367	605	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCF_018491765.1	s__Novosphingobium profundi	80.6254	640	1448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:16,743] [INFO] GTDB search result was written to GCF_022832385.1_ASM2283238v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:16,744] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:16,747] [INFO] DFAST_QC result json was written to GCF_022832385.1_ASM2283238v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:16,747] [INFO] DFAST_QC completed!
[2024-01-25 19:37:16,747] [INFO] Total running time: 0h1m26s