[2024-01-24 14:10:15,629] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:10:15,633] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:10:15,633] [INFO] DQC Reference Directory: /var/lib/cwl/stgb84f9eae-95f9-4c87-9042-c349beda050f/dqc_reference
[2024-01-24 14:10:16,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:10:16,991] [INFO] Task started: Prodigal
[2024-01-24 14:10:16,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg25e46a83-4010-4894-a281-03eb94927c84/GCF_007097155.1_ASM709715v1_genomic.fna.gz | prodigal -d GCF_007097155.1_ASM709715v1_genomic.fna/cds.fna -a GCF_007097155.1_ASM709715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:10:27,174] [INFO] Task succeeded: Prodigal
[2024-01-24 14:10:27,174] [INFO] Task started: HMMsearch
[2024-01-24 14:10:27,175] [INFO] Running command: hmmsearch --tblout GCF_007097155.1_ASM709715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb84f9eae-95f9-4c87-9042-c349beda050f/dqc_reference/reference_markers.hmm GCF_007097155.1_ASM709715v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:10:27,462] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:10:27,463] [INFO] Found 6/6 markers.
[2024-01-24 14:10:27,495] [INFO] Query marker FASTA was written to GCF_007097155.1_ASM709715v1_genomic.fna/markers.fasta
[2024-01-24 14:10:27,496] [INFO] Task started: Blastn
[2024-01-24 14:10:27,496] [INFO] Running command: blastn -query GCF_007097155.1_ASM709715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb84f9eae-95f9-4c87-9042-c349beda050f/dqc_reference/reference_markers.fasta -out GCF_007097155.1_ASM709715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:28,508] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:28,511] [INFO] Selected 24 target genomes.
[2024-01-24 14:10:28,512] [INFO] Target genome list was writen to GCF_007097155.1_ASM709715v1_genomic.fna/target_genomes.txt
[2024-01-24 14:10:28,521] [INFO] Task started: fastANI
[2024-01-24 14:10:28,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e46a83-4010-4894-a281-03eb94927c84/GCF_007097155.1_ASM709715v1_genomic.fna.gz --refList GCF_007097155.1_ASM709715v1_genomic.fna/target_genomes.txt --output GCF_007097155.1_ASM709715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:10:45,788] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:45,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb84f9eae-95f9-4c87-9042-c349beda050f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:10:45,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb84f9eae-95f9-4c87-9042-c349beda050f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:10:45,806] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:10:45,807] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:10:45,807] [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 fuscus	strain=D40P	GCA_009372075.1	1439888	1439888	type	True	78.6904	439	1141	95	below_threshold
Polymorphobacter fuscus	strain=D40P	GCA_009607675.1	1439888	1439888	type	True	78.6767	441	1141	95	below_threshold
Polymorphobacter fuscus	strain=DSM 105347	GCA_011927825.1	1439888	1439888	type	True	78.5682	450	1141	95	below_threshold
Polymorphobacter multimanifer	strain=JCM 18140	GCA_014647295.1	1070431	1070431	type	True	78.1288	336	1141	95	below_threshold
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	77.9947	418	1141	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	77.9501	382	1141	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	77.9472	361	1141	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.8832	398	1141	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	77.7686	305	1141	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	77.7621	376	1141	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	77.7571	358	1141	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.6604	364	1141	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.6586	435	1141	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.6553	337	1141	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	77.6419	333	1141	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	77.5973	365	1141	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	77.5392	419	1141	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	77.4945	370	1141	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	77.4842	348	1141	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	77.4295	355	1141	95	below_threshold
Sphingopyxis granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	77.3806	359	1141	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	77.2543	268	1141	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	77.1475	267	1141	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	77.0877	264	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:10:45,809] [INFO] DFAST Taxonomy check result was written to GCF_007097155.1_ASM709715v1_genomic.fna/tc_result.tsv
[2024-01-24 14:10:45,809] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:10:45,810] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:10:45,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb84f9eae-95f9-4c87-9042-c349beda050f/dqc_reference/checkm_data
[2024-01-24 14:10:45,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:10:45,847] [INFO] Task started: CheckM
[2024-01-24 14:10:45,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007097155.1_ASM709715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007097155.1_ASM709715v1_genomic.fna/checkm_input GCF_007097155.1_ASM709715v1_genomic.fna/checkm_result
[2024-01-24 14:11:17,971] [INFO] Task succeeded: CheckM
[2024-01-24 14:11:17,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:11:17,992] [INFO] ===== Completeness check finished =====
[2024-01-24 14:11:17,992] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:11:17,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007097155.1_ASM709715v1_genomic.fna/markers.fasta)
[2024-01-24 14:11:17,993] [INFO] Task started: Blastn
[2024-01-24 14:11:17,993] [INFO] Running command: blastn -query GCF_007097155.1_ASM709715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb84f9eae-95f9-4c87-9042-c349beda050f/dqc_reference/reference_markers_gtdb.fasta -out GCF_007097155.1_ASM709715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:19,775] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:19,779] [INFO] Selected 11 target genomes.
[2024-01-24 14:11:19,779] [INFO] Target genome list was writen to GCF_007097155.1_ASM709715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:11:19,817] [INFO] Task started: fastANI
[2024-01-24 14:11:19,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e46a83-4010-4894-a281-03eb94927c84/GCF_007097155.1_ASM709715v1_genomic.fna.gz --refList GCF_007097155.1_ASM709715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007097155.1_ASM709715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:11:28,537] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:28,547] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:11:28,547] [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_007097155.1	s__Glacieibacterium frigidum	100.0	1141	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018982925.1	s__Glacieibacterium sp018982925	81.8322	661	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903643075.1	s__CAHJWT01 sp903643075	80.0892	383	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019245455.1	s__CAHJWT01 sp019245455	80.0277	398	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903642255.1	s__CAHJWT01 sp903642255	79.8931	363	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018982885.1	s__CAHJWT01 sp018982885	79.6927	561	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241875.1	s__Polymorphobacter sp003241875	79.0498	504	1141	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	78.8553	469	1141	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_000016765.1	s__Rhizorhabdus wittichii	78.0031	461	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_014643455.1	s__Polymorphobacter glacialis	77.9704	421	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204695.1	s__Sphingomonas sp001897045	77.4887	366	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:11:28,549] [INFO] GTDB search result was written to GCF_007097155.1_ASM709715v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:11:28,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:11:28,554] [INFO] DFAST_QC result json was written to GCF_007097155.1_ASM709715v1_genomic.fna/dqc_result.json
[2024-01-24 14:11:28,554] [INFO] DFAST_QC completed!
[2024-01-24 14:11:28,554] [INFO] Total running time: 0h1m13s