[2024-01-24 12:06:50,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,841] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg655ee013-f079-4c3c-af39-fd2e07a00c7d/dqc_reference
[2024-01-24 12:06:52,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:52,082] [INFO] Task started: Prodigal
[2024-01-24 12:06:52,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg807ecfb9-fa25-45ce-b213-6e9d9180ad28/GCF_011762085.1_ASM1176208v1_genomic.fna.gz | prodigal -d GCF_011762085.1_ASM1176208v1_genomic.fna/cds.fna -a GCF_011762085.1_ASM1176208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:00,580] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:00,580] [INFO] Task started: HMMsearch
[2024-01-24 12:07:00,581] [INFO] Running command: hmmsearch --tblout GCF_011762085.1_ASM1176208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg655ee013-f079-4c3c-af39-fd2e07a00c7d/dqc_reference/reference_markers.hmm GCF_011762085.1_ASM1176208v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:00,838] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:00,841] [INFO] Found 6/6 markers.
[2024-01-24 12:07:00,876] [INFO] Query marker FASTA was written to GCF_011762085.1_ASM1176208v1_genomic.fna/markers.fasta
[2024-01-24 12:07:00,877] [INFO] Task started: Blastn
[2024-01-24 12:07:00,877] [INFO] Running command: blastn -query GCF_011762085.1_ASM1176208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg655ee013-f079-4c3c-af39-fd2e07a00c7d/dqc_reference/reference_markers.fasta -out GCF_011762085.1_ASM1176208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:01,865] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:01,870] [INFO] Selected 22 target genomes.
[2024-01-24 12:07:01,871] [INFO] Target genome list was writen to GCF_011762085.1_ASM1176208v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:01,880] [INFO] Task started: fastANI
[2024-01-24 12:07:01,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg807ecfb9-fa25-45ce-b213-6e9d9180ad28/GCF_011762085.1_ASM1176208v1_genomic.fna.gz --refList GCF_011762085.1_ASM1176208v1_genomic.fna/target_genomes.txt --output GCF_011762085.1_ASM1176208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:18,846] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:18,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg655ee013-f079-4c3c-af39-fd2e07a00c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:18,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg655ee013-f079-4c3c-af39-fd2e07a00c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:18,866] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:18,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:18,867] [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 japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	100.0	954	954	95	conclusive
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	80.5074	585	954	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	80.0956	566	954	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.9967	553	954	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	79.9905	555	954	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.9668	553	954	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.8417	523	954	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	79.7667	518	954	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	79.7626	493	954	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.7484	506	954	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	79.6165	487	954	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.6106	509	954	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	79.55	474	954	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	79.5454	472	954	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	79.466	475	954	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.3842	466	954	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.2941	503	954	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	79.2114	450	954	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	79.1926	463	954	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.0833	483	954	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.0148	510	954	95	below_threshold
Stakelama flava	strain=CBK3Z-3	GCA_019351405.1	2860338	2860338	type	True	78.5736	371	954	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:18,870] [INFO] DFAST Taxonomy check result was written to GCF_011762085.1_ASM1176208v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:18,870] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:18,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:18,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg655ee013-f079-4c3c-af39-fd2e07a00c7d/dqc_reference/checkm_data
[2024-01-24 12:07:18,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:18,905] [INFO] Task started: CheckM
[2024-01-24 12:07:18,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011762085.1_ASM1176208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011762085.1_ASM1176208v1_genomic.fna/checkm_input GCF_011762085.1_ASM1176208v1_genomic.fna/checkm_result
[2024-01-24 12:07:47,990] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:47,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:48,014] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:48,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:48,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011762085.1_ASM1176208v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:48,015] [INFO] Task started: Blastn
[2024-01-24 12:07:48,015] [INFO] Running command: blastn -query GCF_011762085.1_ASM1176208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg655ee013-f079-4c3c-af39-fd2e07a00c7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_011762085.1_ASM1176208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:49,804] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:49,807] [INFO] Selected 27 target genomes.
[2024-01-24 12:07:49,807] [INFO] Target genome list was writen to GCF_011762085.1_ASM1176208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:49,826] [INFO] Task started: fastANI
[2024-01-24 12:07:49,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg807ecfb9-fa25-45ce-b213-6e9d9180ad28/GCF_011762085.1_ASM1176208v1_genomic.fna.gz --refList GCF_011762085.1_ASM1176208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011762085.1_ASM1176208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:09,706] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:09,730] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:09,730] [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_006346325.1	s__Sphingomonas japonica	99.9992	951	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_005144715.1	s__Sphingomonas sp005144715	80.5284	583	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000786205.1	s__Sphingomonas sp000786205	80.2979	533	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001555965.1	s__Sphingomonas sp001555965	80.1834	531	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_002351485.1	s__Sphingomonas spermidinifaciens	80.1148	564	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	79.8668	521	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCA_006438735.1	s__Sphingomonas koreensis_A	79.8317	521	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.05	96.05	0.80	0.80	2	-
GCF_018449795.1	s__Sphingomonas sp018449795	79.8161	517	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797435.1	s__Sphingomonas koreensis	79.8034	514	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCA_003240755.1	s__Sphingomonas hengshuiensis_A	79.791	496	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927635.1	s__Sphingomonas trueperi	79.6332	485	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	98.84	0.92	0.91	3	-
GCF_004341505.2	s__Sphingomonas sp004341505	79.627	456	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_004135605.1	s__Sphingomonas desiccabilis	79.6236	463	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001598435.1	s__Sphingomonas pituitosa	79.5761	472	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421355.1	s__Sphingomonas sp001421355	79.5703	492	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.29	96.58	0.97	0.94	3	-
GCF_000226955.1	s__Sphingomonas elodea_A	79.5527	455	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091475.1	s__Sphingomonas azotifigens	79.5398	473	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425385.1	s__Sphingomonas sp001425385	79.454	549	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.44	96.89	0.96	0.93	3	-
GCF_001421965.1	s__Sphingomonas sp001421965	79.3957	506	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.43	97.43	0.91	0.91	2	-
GCA_002281485.1	s__Sphingomonas sp002281485	79.3633	412	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304615.1	s__Sphingomonas sp017304615	79.3437	449	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013344685.1	s__Sphingomonas sp013344685	79.2862	463	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115745.1	s__Sphingomonas rubra	79.2747	444	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937575.1	s__Sphingomonas aeriglobus	79.2739	465	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217605.1	s__Sphingomonas sp014217605	79.2691	445	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345855.1	s__Sphingomonas sp004345855	79.1812	512	954	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884945.1	s__Sphingomonas sp903884945	79.1143	456	954	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 12:08:09,732] [INFO] GTDB search result was written to GCF_011762085.1_ASM1176208v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:09,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:09,737] [INFO] DFAST_QC result json was written to GCF_011762085.1_ASM1176208v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:09,737] [INFO] DFAST_QC completed!
[2024-01-24 12:08:09,738] [INFO] Total running time: 0h1m19s