[2024-01-24 13:41:19,205] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:19,208] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:19,208] [INFO] DQC Reference Directory: /var/lib/cwl/stga5302e76-7436-4f66-9632-691e4a85f9da/dqc_reference
[2024-01-24 13:41:20,623] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:20,625] [INFO] Task started: Prodigal
[2024-01-24 13:41:20,625] [INFO] Running command: gunzip -c /var/lib/cwl/stg42afb398-b9ca-45cf-9fdb-43471f4edde3/GCF_014199325.1_ASM1419932v1_genomic.fna.gz | prodigal -d GCF_014199325.1_ASM1419932v1_genomic.fna/cds.fna -a GCF_014199325.1_ASM1419932v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:30,906] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:30,906] [INFO] Task started: HMMsearch
[2024-01-24 13:41:30,906] [INFO] Running command: hmmsearch --tblout GCF_014199325.1_ASM1419932v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5302e76-7436-4f66-9632-691e4a85f9da/dqc_reference/reference_markers.hmm GCF_014199325.1_ASM1419932v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:31,183] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:31,184] [INFO] Found 6/6 markers.
[2024-01-24 13:41:31,215] [INFO] Query marker FASTA was written to GCF_014199325.1_ASM1419932v1_genomic.fna/markers.fasta
[2024-01-24 13:41:31,215] [INFO] Task started: Blastn
[2024-01-24 13:41:31,215] [INFO] Running command: blastn -query GCF_014199325.1_ASM1419932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5302e76-7436-4f66-9632-691e4a85f9da/dqc_reference/reference_markers.fasta -out GCF_014199325.1_ASM1419932v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:32,241] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:32,245] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:32,246] [INFO] Target genome list was writen to GCF_014199325.1_ASM1419932v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:32,253] [INFO] Task started: fastANI
[2024-01-24 13:41:32,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg42afb398-b9ca-45cf-9fdb-43471f4edde3/GCF_014199325.1_ASM1419932v1_genomic.fna.gz --refList GCF_014199325.1_ASM1419932v1_genomic.fna/target_genomes.txt --output GCF_014199325.1_ASM1419932v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:48,597] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:48,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5302e76-7436-4f66-9632-691e4a85f9da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:48,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5302e76-7436-4f66-9632-691e4a85f9da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:48,613] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:48,613] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:48,614] [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 yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	100.0	1182	1182	95	conclusive
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	87.2979	874	1182	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	81.388	610	1182	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.9055	509	1182	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	79.8773	506	1182	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.8232	591	1182	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.7932	598	1182	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	79.692	522	1182	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	79.6766	561	1182	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	79.6567	555	1182	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	79.6446	524	1182	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.5518	579	1182	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.5396	584	1182	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.5275	602	1182	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.4209	597	1182	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.187	596	1182	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.1504	533	1182	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	79.1259	521	1182	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	78.6136	484	1182	95	below_threshold
Sphingomonas mucosissima	strain=DSM 17494	GCA_002197665.1	370959	370959	type	True	78.4139	371	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:48,615] [INFO] DFAST Taxonomy check result was written to GCF_014199325.1_ASM1419932v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:48,616] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:48,616] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:48,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5302e76-7436-4f66-9632-691e4a85f9da/dqc_reference/checkm_data
[2024-01-24 13:41:48,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:48,655] [INFO] Task started: CheckM
[2024-01-24 13:41:48,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199325.1_ASM1419932v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199325.1_ASM1419932v1_genomic.fna/checkm_input GCF_014199325.1_ASM1419932v1_genomic.fna/checkm_result
[2024-01-24 13:42:22,159] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:22,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:22,180] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:22,181] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:22,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199325.1_ASM1419932v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:22,181] [INFO] Task started: Blastn
[2024-01-24 13:42:22,182] [INFO] Running command: blastn -query GCF_014199325.1_ASM1419932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5302e76-7436-4f66-9632-691e4a85f9da/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199325.1_ASM1419932v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:24,013] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:24,016] [INFO] Selected 19 target genomes.
[2024-01-24 13:42:24,016] [INFO] Target genome list was writen to GCF_014199325.1_ASM1419932v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:24,028] [INFO] Task started: fastANI
[2024-01-24 13:42:24,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg42afb398-b9ca-45cf-9fdb-43471f4edde3/GCF_014199325.1_ASM1419932v1_genomic.fna.gz --refList GCF_014199325.1_ASM1419932v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199325.1_ASM1419932v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:39,282] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:39,310] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:39,310] [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_014199325.1	s__Sphingomonas yantingensis	100.0	1182	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.75	96.75	0.89	0.89	2	conclusive
GCF_002351485.1	s__Sphingomonas spermidinifaciens	87.3097	873	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144715.1	s__Sphingomonas sp005144715	81.381	611	1182	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	80.0515	577	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_000786205.1	s__Sphingomonas sp000786205	79.9268	556	1182	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	79.8696	512	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115745.1	s__Sphingomonas rubra	79.6819	523	1182	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	79.6645	555	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCA_001897375.1	s__Sphingomonas sp001897375	79.6582	505	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_012035195.1	s__Sphingomonas sp012035195	79.5919	574	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498785.1	s__Sphingomonas sp902498785	79.5679	516	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114095.1	s__Sphingomonas sp900114095	79.5298	587	1182	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	79.4975	546	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCF_006716975.1	s__Sphingomonas trueperi_A	79.4529	576	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.23	95.23	0.88	0.88	2	-
GCF_014194975.1	s__Sphingomonas sp014194975	79.4288	587	1182	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	79.3189	500	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018122655.1	s__Sphingomonas sp018122655	79.1527	475	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707985.1	s__Sphingomonas sp002707985	78.3231	380	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	78.1432	399	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:39,312] [INFO] GTDB search result was written to GCF_014199325.1_ASM1419932v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:39,313] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:39,318] [INFO] DFAST_QC result json was written to GCF_014199325.1_ASM1419932v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:39,318] [INFO] DFAST_QC completed!
[2024-01-24 13:42:39,318] [INFO] Total running time: 0h1m20s