[2024-01-24 13:17:44,228] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:44,230] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:44,230] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe58fa61-2f59-4b88-93a6-e48863945177/dqc_reference
[2024-01-24 13:17:45,521] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:45,522] [INFO] Task started: Prodigal
[2024-01-24 13:17:45,522] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c847f6e-7770-463d-a769-da98ca3571e9/GCF_004792685.1_ASM479268v1_genomic.fna.gz | prodigal -d GCF_004792685.1_ASM479268v1_genomic.fna/cds.fna -a GCF_004792685.1_ASM479268v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:59,085] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:59,085] [INFO] Task started: HMMsearch
[2024-01-24 13:17:59,085] [INFO] Running command: hmmsearch --tblout GCF_004792685.1_ASM479268v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe58fa61-2f59-4b88-93a6-e48863945177/dqc_reference/reference_markers.hmm GCF_004792685.1_ASM479268v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:59,454] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:59,456] [INFO] Found 6/6 markers.
[2024-01-24 13:17:59,514] [INFO] Query marker FASTA was written to GCF_004792685.1_ASM479268v1_genomic.fna/markers.fasta
[2024-01-24 13:17:59,514] [INFO] Task started: Blastn
[2024-01-24 13:17:59,514] [INFO] Running command: blastn -query GCF_004792685.1_ASM479268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe58fa61-2f59-4b88-93a6-e48863945177/dqc_reference/reference_markers.fasta -out GCF_004792685.1_ASM479268v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:00,595] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:00,598] [INFO] Selected 16 target genomes.
[2024-01-24 13:18:00,599] [INFO] Target genome list was writen to GCF_004792685.1_ASM479268v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:00,605] [INFO] Task started: fastANI
[2024-01-24 13:18:00,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c847f6e-7770-463d-a769-da98ca3571e9/GCF_004792685.1_ASM479268v1_genomic.fna.gz --refList GCF_004792685.1_ASM479268v1_genomic.fna/target_genomes.txt --output GCF_004792685.1_ASM479268v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:16,691] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:16,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe58fa61-2f59-4b88-93a6-e48863945177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:16,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe58fa61-2f59-4b88-93a6-e48863945177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:16,706] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:16,706] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:16,706] [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 gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	100.0	1539	1540	95	conclusive
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	87.1572	1136	1540	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	85.5944	1010	1540	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	85.5442	1023	1540	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	81.8126	820	1540	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	81.6898	833	1540	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	81.0229	709	1540	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	80.8563	647	1540	95	below_threshold
Sphingomonas xinjiangensis	strain=DSM 26736	GCA_014199255.1	643568	643568	type	True	80.5406	667	1540	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.5808	592	1540	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.5446	504	1540	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	79.5112	513	1540	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	79.3884	600	1540	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.3272	589	1540	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	78.9696	592	1540	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.3284	527	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:16,707] [INFO] DFAST Taxonomy check result was written to GCF_004792685.1_ASM479268v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:16,708] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:16,708] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:16,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe58fa61-2f59-4b88-93a6-e48863945177/dqc_reference/checkm_data
[2024-01-24 13:18:16,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:16,755] [INFO] Task started: CheckM
[2024-01-24 13:18:16,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004792685.1_ASM479268v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004792685.1_ASM479268v1_genomic.fna/checkm_input GCF_004792685.1_ASM479268v1_genomic.fna/checkm_result
[2024-01-24 13:18:59,538] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:59,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:59,559] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:59,559] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:59,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004792685.1_ASM479268v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:59,560] [INFO] Task started: Blastn
[2024-01-24 13:18:59,560] [INFO] Running command: blastn -query GCF_004792685.1_ASM479268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe58fa61-2f59-4b88-93a6-e48863945177/dqc_reference/reference_markers_gtdb.fasta -out GCF_004792685.1_ASM479268v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:01,399] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:01,402] [INFO] Selected 8 target genomes.
[2024-01-24 13:19:01,403] [INFO] Target genome list was writen to GCF_004792685.1_ASM479268v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:01,416] [INFO] Task started: fastANI
[2024-01-24 13:19:01,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c847f6e-7770-463d-a769-da98ca3571e9/GCF_004792685.1_ASM479268v1_genomic.fna.gz --refList GCF_004792685.1_ASM479268v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004792685.1_ASM479268v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:09,981] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:09,989] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:09,990] [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_004792685.1	s__Sphingomonas gei	100.0	1539	1540	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_002796605.1	s__Sphingomonas sp002796605	87.1561	1137	1540	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	85.669	979	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	85.5455	970	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	85.5226	1025	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002002925.1	s__Sphingomonas sp002002925	85.4941	1017	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135605.1	s__Sphingomonas desiccabilis	79.5344	505	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004341505.2	s__Sphingomonas sp004341505	79.2829	517	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:09,993] [INFO] GTDB search result was written to GCF_004792685.1_ASM479268v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:09,994] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:09,998] [INFO] DFAST_QC result json was written to GCF_004792685.1_ASM479268v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:09,998] [INFO] DFAST_QC completed!
[2024-01-24 13:19:09,998] [INFO] Total running time: 0h1m26s