[2024-01-24 13:46:00,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:00,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:00,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg972f6a02-d052-4324-9a13-1cdbe61f8ef3/dqc_reference
[2024-01-24 13:46:01,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:01,714] [INFO] Task started: Prodigal
[2024-01-24 13:46:01,714] [INFO] Running command: gunzip -c /var/lib/cwl/stge647b0e9-eea3-4a68-86bc-e03d1a40bbb7/GCF_014199625.1_ASM1419962v1_genomic.fna.gz | prodigal -d GCF_014199625.1_ASM1419962v1_genomic.fna/cds.fna -a GCF_014199625.1_ASM1419962v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:14,277] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:14,277] [INFO] Task started: HMMsearch
[2024-01-24 13:46:14,277] [INFO] Running command: hmmsearch --tblout GCF_014199625.1_ASM1419962v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg972f6a02-d052-4324-9a13-1cdbe61f8ef3/dqc_reference/reference_markers.hmm GCF_014199625.1_ASM1419962v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:14,630] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:14,631] [INFO] Found 6/6 markers.
[2024-01-24 13:46:14,691] [INFO] Query marker FASTA was written to GCF_014199625.1_ASM1419962v1_genomic.fna/markers.fasta
[2024-01-24 13:46:14,691] [INFO] Task started: Blastn
[2024-01-24 13:46:14,691] [INFO] Running command: blastn -query GCF_014199625.1_ASM1419962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg972f6a02-d052-4324-9a13-1cdbe61f8ef3/dqc_reference/reference_markers.fasta -out GCF_014199625.1_ASM1419962v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:15,800] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:15,806] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:15,807] [INFO] Target genome list was writen to GCF_014199625.1_ASM1419962v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:15,813] [INFO] Task started: fastANI
[2024-01-24 13:46:15,813] [INFO] Running command: fastANI --query /var/lib/cwl/stge647b0e9-eea3-4a68-86bc-e03d1a40bbb7/GCF_014199625.1_ASM1419962v1_genomic.fna.gz --refList GCF_014199625.1_ASM1419962v1_genomic.fna/target_genomes.txt --output GCF_014199625.1_ASM1419962v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:35,291] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:35,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg972f6a02-d052-4324-9a13-1cdbe61f8ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:35,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg972f6a02-d052-4324-9a13-1cdbe61f8ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:35,309] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:35,309] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:35,310] [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 abaci	strain=DSM 15867	GCA_014199625.1	237611	237611	type	True	100.0	1447	1449	95	conclusive
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	82.5086	759	1449	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	81.9787	674	1449	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	81.7642	694	1449	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	81.6916	690	1449	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	81.641	760	1449	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	81.5109	649	1449	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	81.3931	740	1449	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	81.344	718	1449	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_017052355.1	413712	413712	type	True	81.3304	732	1449	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	81.2774	751	1449	95	below_threshold
Sphingomonas paucimobilis	strain=FDAARGOS_908	GCA_016027095.1	13689	13689	type	True	81.1906	723	1449	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	81.102	719	1449	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	80.9881	670	1449	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	80.793	624	1449	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.7909	748	1449	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	80.7527	698	1449	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	80.1289	696	1449	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.5495	575	1449	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.361	621	1449	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	78.7577	519	1449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:35,311] [INFO] DFAST Taxonomy check result was written to GCF_014199625.1_ASM1419962v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:35,312] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:35,312] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:35,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg972f6a02-d052-4324-9a13-1cdbe61f8ef3/dqc_reference/checkm_data
[2024-01-24 13:46:35,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:35,356] [INFO] Task started: CheckM
[2024-01-24 13:46:35,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199625.1_ASM1419962v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199625.1_ASM1419962v1_genomic.fna/checkm_input GCF_014199625.1_ASM1419962v1_genomic.fna/checkm_result
[2024-01-24 13:47:17,657] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:17,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:17,681] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:17,682] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:17,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199625.1_ASM1419962v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:17,682] [INFO] Task started: Blastn
[2024-01-24 13:47:17,682] [INFO] Running command: blastn -query GCF_014199625.1_ASM1419962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg972f6a02-d052-4324-9a13-1cdbe61f8ef3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199625.1_ASM1419962v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:19,668] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:19,671] [INFO] Selected 20 target genomes.
[2024-01-24 13:47:19,671] [INFO] Target genome list was writen to GCF_014199625.1_ASM1419962v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:19,688] [INFO] Task started: fastANI
[2024-01-24 13:47:19,688] [INFO] Running command: fastANI --query /var/lib/cwl/stge647b0e9-eea3-4a68-86bc-e03d1a40bbb7/GCF_014199625.1_ASM1419962v1_genomic.fna.gz --refList GCF_014199625.1_ASM1419962v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199625.1_ASM1419962v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:37,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:37,957] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:37,957] [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_014199625.1	s__Sphingomonas abaci	100.0	1447	1449	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_003951315.1	s__Sphingomonas sp003951315	90.0192	1062	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641735.1	s__Sphingomonas metalli	82.5261	760	1449	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	81.9847	673	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841615.1	s__Sphingomonas sp014841615	81.7432	727	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003075315.1	s__Sphingomonas sp003075315	81.6506	727	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCF_000632225.1	s__Sphingomonas sp000632225	81.4084	760	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196115.1	s__Sphingomonas aquatilis	81.3784	715	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCF_000764535.1	s__Sphingomonas taxi	81.3714	743	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_001591005.1	s__Sphingomonas sanguinis	81.3521	714	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.09	96.84	0.89	0.83	8	-
GCF_014196255.1	s__Sphingomonas pseudosanguinis	81.2735	752	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018139225.1	s__Sphingomonas sp018139225	81.1492	712	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000739895.2	s__Sphingomonas paucimobilis	81.1021	720	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.74	99.40	0.92	0.87	13	-
GCF_014197105.1	s__Sphingomonas jinjuensis	80.9822	672	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903644135.1	s__Sphingomonas sp903644135	80.7824	379	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243195.1	s__Sphingomonas taxi_B	80.6238	637	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	80.5089	578	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_014194975.1	s__Sphingomonas sp014194975	80.4762	715	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	80.1885	705	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_001421355.1	s__Sphingomonas sp001421355	79.503	600	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.29	96.58	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:37,959] [INFO] GTDB search result was written to GCF_014199625.1_ASM1419962v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:37,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:37,963] [INFO] DFAST_QC result json was written to GCF_014199625.1_ASM1419962v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:37,964] [INFO] DFAST_QC completed!
[2024-01-24 13:47:37,964] [INFO] Total running time: 0h1m38s