[2024-01-24 14:02:47,301] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:47,303] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:47,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg95069d70-9bb3-4b04-b618-23c3cc89db39/dqc_reference
[2024-01-24 14:02:48,561] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:48,562] [INFO] Task started: Prodigal
[2024-01-24 14:02:48,562] [INFO] Running command: gunzip -c /var/lib/cwl/stg778929b9-79f0-41d5-a6dc-405b0cfe4b77/GCF_014196115.1_ASM1419611v1_genomic.fna.gz | prodigal -d GCF_014196115.1_ASM1419611v1_genomic.fna/cds.fna -a GCF_014196115.1_ASM1419611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:00,634] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:00,635] [INFO] Task started: HMMsearch
[2024-01-24 14:03:00,635] [INFO] Running command: hmmsearch --tblout GCF_014196115.1_ASM1419611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95069d70-9bb3-4b04-b618-23c3cc89db39/dqc_reference/reference_markers.hmm GCF_014196115.1_ASM1419611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:00,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:00,922] [INFO] Found 6/6 markers.
[2024-01-24 14:03:00,959] [INFO] Query marker FASTA was written to GCF_014196115.1_ASM1419611v1_genomic.fna/markers.fasta
[2024-01-24 14:03:00,959] [INFO] Task started: Blastn
[2024-01-24 14:03:00,959] [INFO] Running command: blastn -query GCF_014196115.1_ASM1419611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95069d70-9bb3-4b04-b618-23c3cc89db39/dqc_reference/reference_markers.fasta -out GCF_014196115.1_ASM1419611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:02,049] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:02,052] [INFO] Selected 14 target genomes.
[2024-01-24 14:03:02,053] [INFO] Target genome list was writen to GCF_014196115.1_ASM1419611v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:02,058] [INFO] Task started: fastANI
[2024-01-24 14:03:02,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg778929b9-79f0-41d5-a6dc-405b0cfe4b77/GCF_014196115.1_ASM1419611v1_genomic.fna.gz --refList GCF_014196115.1_ASM1419611v1_genomic.fna/target_genomes.txt --output GCF_014196115.1_ASM1419611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:15,866] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:15,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95069d70-9bb3-4b04-b618-23c3cc89db39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:15,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95069d70-9bb3-4b04-b618-23c3cc89db39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:15,886] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:03:15,886] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:03:15,887] [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 aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	100.0	1293	1298	95	inconclusive
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	99.8632	1168	1298	95	inconclusive
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	95.9856	1096	1298	95	inconclusive
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	84.6933	818	1298	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	84.0078	811	1298	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	81.3395	696	1298	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	81.0848	669	1298	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	80.9264	657	1298	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	80.9027	655	1298	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.3615	619	1298	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.2512	645	1298	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	80.224	623	1298	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.8156	576	1298	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.7787	592	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:15,888] [INFO] DFAST Taxonomy check result was written to GCF_014196115.1_ASM1419611v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:15,889] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:15,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:15,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95069d70-9bb3-4b04-b618-23c3cc89db39/dqc_reference/checkm_data
[2024-01-24 14:03:15,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:15,938] [INFO] Task started: CheckM
[2024-01-24 14:03:15,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196115.1_ASM1419611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196115.1_ASM1419611v1_genomic.fna/checkm_input GCF_014196115.1_ASM1419611v1_genomic.fna/checkm_result
[2024-01-24 14:03:51,844] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:51,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:51,866] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:51,867] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:51,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196115.1_ASM1419611v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:51,868] [INFO] Task started: Blastn
[2024-01-24 14:03:51,868] [INFO] Running command: blastn -query GCF_014196115.1_ASM1419611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95069d70-9bb3-4b04-b618-23c3cc89db39/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196115.1_ASM1419611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:53,854] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:53,858] [INFO] Selected 13 target genomes.
[2024-01-24 14:03:53,859] [INFO] Target genome list was writen to GCF_014196115.1_ASM1419611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:03:53,872] [INFO] Task started: fastANI
[2024-01-24 14:03:53,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg778929b9-79f0-41d5-a6dc-405b0cfe4b77/GCF_014196115.1_ASM1419611v1_genomic.fna.gz --refList GCF_014196115.1_ASM1419611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196115.1_ASM1419611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:07,079] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:07,095] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:07,095] [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_014196115.1	s__Sphingomonas aquatilis	100.0	1293	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	conclusive
GCA_003075315.1	s__Sphingomonas sp003075315	93.783	1100	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCA_002292295.1	s__Sphingomonas sp002292295	84.9299	829	1298	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	84.6835	819	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_013409985.1	s__Sphingomonas melonis_A	84.5458	810	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632225.1	s__Sphingomonas sp000632225	84.141	801	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355005.1	s__Sphingomonas sp003355005	84.073	806	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107325.1	s__Sphingomonas sp016107325	83.146	818	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197105.1	s__Sphingomonas jinjuensis	81.3159	699	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995065.1	s__Sphingomonas ginsenosidivorax	81.0387	674	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476905.1	s__Sphingomonas sanguinis_B	81.006	617	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	-
GCF_014196255.1	s__Sphingomonas pseudosanguinis	80.899	678	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004340945.1	s__Sphingomonas sp004340945	79.8764	649	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.25	95.25	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:07,097] [INFO] GTDB search result was written to GCF_014196115.1_ASM1419611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:07,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:07,104] [INFO] DFAST_QC result json was written to GCF_014196115.1_ASM1419611v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:07,104] [INFO] DFAST_QC completed!
[2024-01-24 14:04:07,105] [INFO] Total running time: 0h1m20s