[2024-01-24 14:32:30,433] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:30,444] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:30,445] [INFO] DQC Reference Directory: /var/lib/cwl/stga944fa91-12fc-4c24-bb7e-12be13c50015/dqc_reference
[2024-01-24 14:32:31,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:31,708] [INFO] Task started: Prodigal
[2024-01-24 14:32:31,708] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5a82dd4-7941-46a8-acae-20d2c0fff035/GCF_014643455.1_ASM1464345v1_genomic.fna.gz | prodigal -d GCF_014643455.1_ASM1464345v1_genomic.fna/cds.fna -a GCF_014643455.1_ASM1464345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:32:41,613] [INFO] Task succeeded: Prodigal
[2024-01-24 14:32:41,613] [INFO] Task started: HMMsearch
[2024-01-24 14:32:41,613] [INFO] Running command: hmmsearch --tblout GCF_014643455.1_ASM1464345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga944fa91-12fc-4c24-bb7e-12be13c50015/dqc_reference/reference_markers.hmm GCF_014643455.1_ASM1464345v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:32:41,896] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:32:41,897] [INFO] Found 6/6 markers.
[2024-01-24 14:32:41,926] [INFO] Query marker FASTA was written to GCF_014643455.1_ASM1464345v1_genomic.fna/markers.fasta
[2024-01-24 14:32:41,927] [INFO] Task started: Blastn
[2024-01-24 14:32:41,927] [INFO] Running command: blastn -query GCF_014643455.1_ASM1464345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga944fa91-12fc-4c24-bb7e-12be13c50015/dqc_reference/reference_markers.fasta -out GCF_014643455.1_ASM1464345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:42,884] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:42,888] [INFO] Selected 18 target genomes.
[2024-01-24 14:32:42,889] [INFO] Target genome list was writen to GCF_014643455.1_ASM1464345v1_genomic.fna/target_genomes.txt
[2024-01-24 14:32:42,897] [INFO] Task started: fastANI
[2024-01-24 14:32:42,898] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5a82dd4-7941-46a8-acae-20d2c0fff035/GCF_014643455.1_ASM1464345v1_genomic.fna.gz --refList GCF_014643455.1_ASM1464345v1_genomic.fna/target_genomes.txt --output GCF_014643455.1_ASM1464345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:56,065] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:56,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga944fa91-12fc-4c24-bb7e-12be13c50015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:56,066] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga944fa91-12fc-4c24-bb7e-12be13c50015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:56,087] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:32:56,087] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:32:56,087] [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
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	100.0	1084	1086	95	conclusive
Polymorphobacter fuscus	strain=D40P	GCA_009372075.1	1439888	1439888	type	True	80.5729	584	1086	95	below_threshold
Polymorphobacter fuscus	strain=D40P	GCA_009607675.1	1439888	1439888	type	True	80.5626	585	1086	95	below_threshold
Polymorphobacter fuscus	strain=DSM 105347	GCA_011927825.1	1439888	1439888	type	True	80.4481	592	1086	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	79.003	424	1086	95	below_threshold
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	78.3159	310	1086	95	below_threshold
Sandarakinorhabdus rubra	strain=MO-4	GCA_010994245.1	2672568	2672568	type	True	78.1555	279	1086	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	77.3014	248	1086	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	76.9287	181	1086	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	76.8828	250	1086	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	76.7877	223	1086	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	76.7669	214	1086	95	below_threshold
Sphingomonas asaccharolytica	strain=NBRC 15499	GCA_001598355.1	40681	40681	type	True	76.7448	223	1086	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	76.7204	165	1086	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	76.466	233	1086	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.7939	133	1086	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.7345	110	1086	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.6691	194	1086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:56,089] [INFO] DFAST Taxonomy check result was written to GCF_014643455.1_ASM1464345v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:56,090] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:56,090] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:56,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga944fa91-12fc-4c24-bb7e-12be13c50015/dqc_reference/checkm_data
[2024-01-24 14:32:56,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:56,129] [INFO] Task started: CheckM
[2024-01-24 14:32:56,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643455.1_ASM1464345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643455.1_ASM1464345v1_genomic.fna/checkm_input GCF_014643455.1_ASM1464345v1_genomic.fna/checkm_result
[2024-01-24 14:33:28,973] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:28,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:28,996] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:28,997] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:28,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643455.1_ASM1464345v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:28,997] [INFO] Task started: Blastn
[2024-01-24 14:33:28,998] [INFO] Running command: blastn -query GCF_014643455.1_ASM1464345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga944fa91-12fc-4c24-bb7e-12be13c50015/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643455.1_ASM1464345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:30,860] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:30,863] [INFO] Selected 14 target genomes.
[2024-01-24 14:33:30,864] [INFO] Target genome list was writen to GCF_014643455.1_ASM1464345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:30,877] [INFO] Task started: fastANI
[2024-01-24 14:33:30,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5a82dd4-7941-46a8-acae-20d2c0fff035/GCF_014643455.1_ASM1464345v1_genomic.fna.gz --refList GCF_014643455.1_ASM1464345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643455.1_ASM1464345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:40,768] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:40,787] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:40,787] [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_014643455.1	s__Polymorphobacter glacialis	100.0	1084	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003241875.1	s__Polymorphobacter sp003241875	81.3312	629	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927825.1	s__Polymorphobacter fuscus	80.464	590	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	99.98	99.98	1.00	1.00	3	-
GCA_002256005.1	s__Polymorphobacter sp002256005	79.8554	522	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903939555.1	s__Polymorphobacter sp903939555	79.6039	378	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	98.54	98.06	0.84	0.82	4	-
GCA_001295935.1	s__Polymorphobacter sp001295935	79.592	475	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298745.1	s__Polymorphobacter sp013298745	79.0554	346	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423025.1	s__Polymorphobacter sp002423025	79.0194	427	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681125.1	s__Polymorphobacter_A arshaanensis	78.3337	372	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097155.1	s__Glacieibacterium frigidum	78.2291	390	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018982925.1	s__Glacieibacterium sp018982925	78.187	396	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018982885.1	s__CAHJWT01 sp018982885	77.9362	362	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331245.1	s__Blastomonas sp000331245	76.862	171	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422985.1	s__Sandaracinobacter sp002422985	76.0257	103	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:40,789] [INFO] GTDB search result was written to GCF_014643455.1_ASM1464345v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:40,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:40,797] [INFO] DFAST_QC result json was written to GCF_014643455.1_ASM1464345v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:40,798] [INFO] DFAST_QC completed!
[2024-01-24 14:33:40,798] [INFO] Total running time: 0h1m10s