[2024-01-24 12:46:53,316] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:53,318] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:53,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg09a39e13-0093-4312-965e-60bb0c094eb2/dqc_reference
[2024-01-24 12:46:54,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:54,578] [INFO] Task started: Prodigal
[2024-01-24 12:46:54,578] [INFO] Running command: gunzip -c /var/lib/cwl/stga7649544-65f7-4457-9d05-2d82bb67f815/GCF_019793235.1_ASM1979323v1_genomic.fna.gz | prodigal -d GCF_019793235.1_ASM1979323v1_genomic.fna/cds.fna -a GCF_019793235.1_ASM1979323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:03,682] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:03,683] [INFO] Task started: HMMsearch
[2024-01-24 12:47:03,683] [INFO] Running command: hmmsearch --tblout GCF_019793235.1_ASM1979323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09a39e13-0093-4312-965e-60bb0c094eb2/dqc_reference/reference_markers.hmm GCF_019793235.1_ASM1979323v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:03,950] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:03,952] [INFO] Found 6/6 markers.
[2024-01-24 12:47:03,980] [INFO] Query marker FASTA was written to GCF_019793235.1_ASM1979323v1_genomic.fna/markers.fasta
[2024-01-24 12:47:03,981] [INFO] Task started: Blastn
[2024-01-24 12:47:03,981] [INFO] Running command: blastn -query GCF_019793235.1_ASM1979323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09a39e13-0093-4312-965e-60bb0c094eb2/dqc_reference/reference_markers.fasta -out GCF_019793235.1_ASM1979323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:04,948] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:04,951] [INFO] Selected 19 target genomes.
[2024-01-24 12:47:04,952] [INFO] Target genome list was writen to GCF_019793235.1_ASM1979323v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:04,959] [INFO] Task started: fastANI
[2024-01-24 12:47:04,959] [INFO] Running command: fastANI --query /var/lib/cwl/stga7649544-65f7-4457-9d05-2d82bb67f815/GCF_019793235.1_ASM1979323v1_genomic.fna.gz --refList GCF_019793235.1_ASM1979323v1_genomic.fna/target_genomes.txt --output GCF_019793235.1_ASM1979323v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:20,512] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:20,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09a39e13-0093-4312-965e-60bb0c094eb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:20,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09a39e13-0093-4312-965e-60bb0c094eb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:20,539] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:20,540] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:20,540] [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
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	84.3288	731	1022	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	84.2376	738	1022	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	83.8634	752	1022	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	83.7365	714	1022	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	83.6307	702	1022	95	below_threshold
Sphingopyxis panaciterrulae	strain=DSM 27163	GCA_014199295.1	462372	462372	type	True	83.521	748	1022	95	below_threshold
Sphingopyxis granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	83.5066	674	1022	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	83.4881	746	1022	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	83.4246	785	1022	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	83.3974	716	1022	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	83.3833	716	1022	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	83.3204	725	1022	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	83.2969	777	1022	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	83.2606	732	1022	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.3801	357	1022	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.8688	232	1022	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.8102	244	1022	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.7082	300	1022	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.5409	276	1022	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:20,542] [INFO] DFAST Taxonomy check result was written to GCF_019793235.1_ASM1979323v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:20,543] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:20,544] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:20,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09a39e13-0093-4312-965e-60bb0c094eb2/dqc_reference/checkm_data
[2024-01-24 12:47:20,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:20,590] [INFO] Task started: CheckM
[2024-01-24 12:47:20,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019793235.1_ASM1979323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019793235.1_ASM1979323v1_genomic.fna/checkm_input GCF_019793235.1_ASM1979323v1_genomic.fna/checkm_result
[2024-01-24 12:47:51,076] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:51,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:51,093] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:51,094] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:51,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019793235.1_ASM1979323v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:51,095] [INFO] Task started: Blastn
[2024-01-24 12:47:51,095] [INFO] Running command: blastn -query GCF_019793235.1_ASM1979323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09a39e13-0093-4312-965e-60bb0c094eb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_019793235.1_ASM1979323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:52,926] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:52,930] [INFO] Selected 23 target genomes.
[2024-01-24 12:47:52,930] [INFO] Target genome list was writen to GCF_019793235.1_ASM1979323v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:52,951] [INFO] Task started: fastANI
[2024-01-24 12:47:52,951] [INFO] Running command: fastANI --query /var/lib/cwl/stga7649544-65f7-4457-9d05-2d82bb67f815/GCF_019793235.1_ASM1979323v1_genomic.fna.gz --refList GCF_019793235.1_ASM1979323v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019793235.1_ASM1979323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:13,083] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:13,105] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:13,106] [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_016734905.1	s__Sphingopyxis sp016734905	98.9886	960	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000013985.1	s__Sphingopyxis alaskensis	84.2854	735	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188185.1	s__Sphingopyxis indica	84.2644	736	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078365.1	s__Sphingopyxis sp900078365	84.2411	777	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756375.1	s__Sphingopyxis sp000756375	83.9301	773	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011926545.1	s__Sphingopyxis italica	83.8505	753	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795895.1	s__Sphingopyxis sp004795895	83.7272	781	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503215.1	s__Sphingopyxis sp005503215	83.6432	784	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.20	99.20	0.88	0.88	2	-
GCF_001990265.1	s__Sphingopyxis sp001990265	83.6294	697	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018682675.1	s__Sphingopyxis soli	83.6168	704	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199295.1	s__Sphingopyxis panaciterrulae	83.521	748	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591045.1	s__Sphingopyxis granuli	83.515	672	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.56	96.77	0.81	0.78	6	-
GCF_001468395.1	s__Sphingopyxis sp001468395	83.496	733	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.27	97.10	0.97	0.89	9	-
GCF_012274265.1	s__Sphingopyxis microcysteis	83.476	747	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.26	96.26	0.86	0.86	2	-
GCF_005503695.1	s__Sphingopyxis sp003609815	83.326	732	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.15	97.15	0.90	0.90	2	-
GCF_000803645.1	s__Sphingopyxis fribergensis	83.3141	775	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793775.1	s__Sphingopyxis sp016793775	83.2482	703	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797775.2	s__Sphingopyxis sp001427085	83.1848	768	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.11	97.01	0.89	0.87	3	-
GCA_001830555.1	s__Sphingopyxis sp001830555	83.1771	716	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463645.1	s__Sphingopyxis sp016463645	83.1141	671	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017309275.1	s__Sphingopyxis sp017309275	83.0441	709	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842935.1	s__Sphingopyxis sp002842935	82.9759	476	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463225.1	s__Sphingopyxis sp016463225	82.7882	708	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:13,107] [INFO] GTDB search result was written to GCF_019793235.1_ASM1979323v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:13,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:13,112] [INFO] DFAST_QC result json was written to GCF_019793235.1_ASM1979323v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:13,112] [INFO] DFAST_QC completed!
[2024-01-24 12:48:13,112] [INFO] Total running time: 0h1m20s