[2024-01-24 12:40:20,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,958] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c821179-6e6f-4bc1-839b-e04d7398ce7b/dqc_reference
[2024-01-24 12:40:22,155] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:22,155] [INFO] Task started: Prodigal
[2024-01-24 12:40:22,156] [INFO] Running command: gunzip -c /var/lib/cwl/stg43e06e98-d9c1-4e40-9df3-a168584065ea/GCF_001598355.1_ASM159835v1_genomic.fna.gz | prodigal -d GCF_001598355.1_ASM159835v1_genomic.fna/cds.fna -a GCF_001598355.1_ASM159835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:34,687] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:34,688] [INFO] Task started: HMMsearch
[2024-01-24 12:40:34,688] [INFO] Running command: hmmsearch --tblout GCF_001598355.1_ASM159835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c821179-6e6f-4bc1-839b-e04d7398ce7b/dqc_reference/reference_markers.hmm GCF_001598355.1_ASM159835v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:34,991] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:34,993] [INFO] Found 6/6 markers.
[2024-01-24 12:40:35,044] [INFO] Query marker FASTA was written to GCF_001598355.1_ASM159835v1_genomic.fna/markers.fasta
[2024-01-24 12:40:35,044] [INFO] Task started: Blastn
[2024-01-24 12:40:35,045] [INFO] Running command: blastn -query GCF_001598355.1_ASM159835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c821179-6e6f-4bc1-839b-e04d7398ce7b/dqc_reference/reference_markers.fasta -out GCF_001598355.1_ASM159835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:35,946] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:35,949] [INFO] Selected 16 target genomes.
[2024-01-24 12:40:35,950] [INFO] Target genome list was writen to GCF_001598355.1_ASM159835v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:35,957] [INFO] Task started: fastANI
[2024-01-24 12:40:35,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg43e06e98-d9c1-4e40-9df3-a168584065ea/GCF_001598355.1_ASM159835v1_genomic.fna.gz --refList GCF_001598355.1_ASM159835v1_genomic.fna/target_genomes.txt --output GCF_001598355.1_ASM159835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:49,587] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:49,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c821179-6e6f-4bc1-839b-e04d7398ce7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:49,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c821179-6e6f-4bc1-839b-e04d7398ce7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:49,606] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:49,606] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:49,606] [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
Sphingomonas asaccharolytica	strain=NBRC 15499	GCA_001598355.1	40681	40681	type	True	100.0	1429	1440	95	conclusive
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	90.3434	1151	1440	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	88.501	1021	1440	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	81.6967	716	1440	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.5563	613	1440	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	79.5262	560	1440	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.5101	562	1440	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.5093	614	1440	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.3772	608	1440	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	79.3734	529	1440	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.2431	455	1440	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	79.0755	563	1440	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.8992	502	1440	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	78.6122	438	1440	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.3679	462	1440	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.0642	354	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:49,608] [INFO] DFAST Taxonomy check result was written to GCF_001598355.1_ASM159835v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:49,608] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:49,608] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:49,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c821179-6e6f-4bc1-839b-e04d7398ce7b/dqc_reference/checkm_data
[2024-01-24 12:40:49,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:49,656] [INFO] Task started: CheckM
[2024-01-24 12:40:49,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001598355.1_ASM159835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001598355.1_ASM159835v1_genomic.fna/checkm_input GCF_001598355.1_ASM159835v1_genomic.fna/checkm_result
[2024-01-24 12:41:27,272] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:27,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:27,293] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:27,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:27,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001598355.1_ASM159835v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:27,295] [INFO] Task started: Blastn
[2024-01-24 12:41:27,295] [INFO] Running command: blastn -query GCF_001598355.1_ASM159835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c821179-6e6f-4bc1-839b-e04d7398ce7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001598355.1_ASM159835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:29,026] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:29,030] [INFO] Selected 13 target genomes.
[2024-01-24 12:41:29,031] [INFO] Target genome list was writen to GCF_001598355.1_ASM159835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:29,040] [INFO] Task started: fastANI
[2024-01-24 12:41:29,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg43e06e98-d9c1-4e40-9df3-a168584065ea/GCF_001598355.1_ASM159835v1_genomic.fna.gz --refList GCF_001598355.1_ASM159835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001598355.1_ASM159835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:40,605] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:40,617] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:40,617] [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_001598355.1	s__Sphingomonas asaccharolytica	100.0	1429	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001598415.1	s__Sphingomonas mali	90.3573	1150	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598455.1	s__Sphingomonas pruni	88.5112	1021	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799495.1	s__Sphingomonas sp004799495	81.8449	677	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859635.1	s__Sphingomonas panacisoli	81.6967	716	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304635.1	s__Sphingomonas sp017304635	81.5528	644	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240825.1	s__Sphingomonas sp018240825	81.2532	432	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449795.1	s__Sphingomonas sp018449795	79.4853	544	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489075.1	s__Sphingomonas sp014489075	79.4143	603	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001717955.1	s__Sphingomonas panacis	79.3833	528	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428865.1	s__Sphingomonas sp001428865	79.3522	568	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744835.1	s__Sphingomonas sp017744835	79.2159	518	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	78.8907	498	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:40,619] [INFO] GTDB search result was written to GCF_001598355.1_ASM159835v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:40,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:40,625] [INFO] DFAST_QC result json was written to GCF_001598355.1_ASM159835v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:40,626] [INFO] DFAST_QC completed!
[2024-01-24 12:41:40,626] [INFO] Total running time: 0h1m20s