[2024-01-24 14:38:46,998] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:47,010] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:47,011] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5204eb8-7d4c-4f4b-adf2-e0b87ce25931/dqc_reference
[2024-01-24 14:38:48,336] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,360] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,361] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d2a0c38-f7ee-45cc-9d4d-f019acea953f/GCF_001590985.1_ASM159098v1_genomic.fna.gz | prodigal -d GCF_001590985.1_ASM159098v1_genomic.fna/cds.fna -a GCF_001590985.1_ASM159098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:03,984] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:03,984] [INFO] Task started: HMMsearch
[2024-01-24 14:39:03,984] [INFO] Running command: hmmsearch --tblout GCF_001590985.1_ASM159098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5204eb8-7d4c-4f4b-adf2-e0b87ce25931/dqc_reference/reference_markers.hmm GCF_001590985.1_ASM159098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:04,291] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:04,292] [INFO] Found 6/6 markers.
[2024-01-24 14:39:04,338] [INFO] Query marker FASTA was written to GCF_001590985.1_ASM159098v1_genomic.fna/markers.fasta
[2024-01-24 14:39:04,338] [INFO] Task started: Blastn
[2024-01-24 14:39:04,339] [INFO] Running command: blastn -query GCF_001590985.1_ASM159098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5204eb8-7d4c-4f4b-adf2-e0b87ce25931/dqc_reference/reference_markers.fasta -out GCF_001590985.1_ASM159098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:05,374] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:05,378] [INFO] Selected 16 target genomes.
[2024-01-24 14:39:05,379] [INFO] Target genome list was writen to GCF_001590985.1_ASM159098v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:05,386] [INFO] Task started: fastANI
[2024-01-24 14:39:05,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d2a0c38-f7ee-45cc-9d4d-f019acea953f/GCF_001590985.1_ASM159098v1_genomic.fna.gz --refList GCF_001590985.1_ASM159098v1_genomic.fna/target_genomes.txt --output GCF_001590985.1_ASM159098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:21,062] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:21,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5204eb8-7d4c-4f4b-adf2-e0b87ce25931/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:21,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5204eb8-7d4c-4f4b-adf2-e0b87ce25931/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:21,078] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:21,079] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:21,079] [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	100.0	1632	1637	95	conclusive
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	83.8275	869	1637	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	83.0869	797	1637	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	82.2769	730	1637	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	82.2155	739	1637	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	81.7716	617	1637	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	81.6473	705	1637	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	81.2746	652	1637	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	81.2627	629	1637	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	80.9945	668	1637	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	80.9345	685	1637	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	80.803	608	1637	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	80.6634	637	1637	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.9204	567	1637	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.8474	507	1637	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.8138	511	1637	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:21,081] [INFO] DFAST Taxonomy check result was written to GCF_001590985.1_ASM159098v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:21,081] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:21,081] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:21,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5204eb8-7d4c-4f4b-adf2-e0b87ce25931/dqc_reference/checkm_data
[2024-01-24 14:39:21,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:21,135] [INFO] Task started: CheckM
[2024-01-24 14:39:21,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001590985.1_ASM159098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001590985.1_ASM159098v1_genomic.fna/checkm_input GCF_001590985.1_ASM159098v1_genomic.fna/checkm_result
[2024-01-24 14:40:08,604] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:08,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:08,629] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:08,630] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:08,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001590985.1_ASM159098v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:08,631] [INFO] Task started: Blastn
[2024-01-24 14:40:08,631] [INFO] Running command: blastn -query GCF_001590985.1_ASM159098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5204eb8-7d4c-4f4b-adf2-e0b87ce25931/dqc_reference/reference_markers_gtdb.fasta -out GCF_001590985.1_ASM159098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:10,947] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:10,951] [INFO] Selected 15 target genomes.
[2024-01-24 14:40:10,951] [INFO] Target genome list was writen to GCF_001590985.1_ASM159098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:10,964] [INFO] Task started: fastANI
[2024-01-24 14:40:10,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d2a0c38-f7ee-45cc-9d4d-f019acea953f/GCF_001590985.1_ASM159098v1_genomic.fna.gz --refList GCF_001590985.1_ASM159098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001590985.1_ASM159098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:28,127] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:28,141] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:28,141] [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	100.0	1632	1637	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_014645195.1	s__Novosphingobium indicum	83.8353	868	1637	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	83.087	797	1637	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	82.6543	740	1637	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	82.3009	728	1637	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	82.0439	642	1637	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	82.0256	608	1637	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	81.9731	758	1637	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_002149965.1	s__Novosphingobium panipatense	81.823	703	1637	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.24	97.74	0.85	0.82	3	-
GCF_000281975.1	s__Novosphingobium sp000281975	81.6961	664	1637	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	81.6473	705	1637	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.03	99.03	0.83	0.83	2	-
GCF_015865035.1	s__Novosphingobium sp015865035	81.2912	650	1637	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018491765.1	s__Novosphingobium profundi	80.9412	684	1637	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272475.1	s__Novosphingobium sp000272475	80.4611	561	1637	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009746585.1	s__Novosphingobium sp009746585	79.916	567	1637	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 14:40:28,147] [INFO] GTDB search result was written to GCF_001590985.1_ASM159098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:28,148] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:28,152] [INFO] DFAST_QC result json was written to GCF_001590985.1_ASM159098v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:28,152] [INFO] DFAST_QC completed!
[2024-01-24 14:40:28,152] [INFO] Total running time: 0h1m41s