[2024-01-24 10:47:11,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg552e5a7d-8101-4dd3-afd4-49bc3a09cbde/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,945] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb593d22-6af8-405a-8175-8e12d279b528/GCF_012274265.1_ASM1227426v1_genomic.fna.gz | prodigal -d GCF_012274265.1_ASM1227426v1_genomic.fna/cds.fna -a GCF_012274265.1_ASM1227426v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:29,281] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:29,281] [INFO] Task started: HMMsearch
[2024-01-24 10:47:29,281] [INFO] Running command: hmmsearch --tblout GCF_012274265.1_ASM1227426v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg552e5a7d-8101-4dd3-afd4-49bc3a09cbde/dqc_reference/reference_markers.hmm GCF_012274265.1_ASM1227426v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:29,528] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:29,530] [INFO] Found 6/6 markers.
[2024-01-24 10:47:29,566] [INFO] Query marker FASTA was written to GCF_012274265.1_ASM1227426v1_genomic.fna/markers.fasta
[2024-01-24 10:47:29,566] [INFO] Task started: Blastn
[2024-01-24 10:47:29,566] [INFO] Running command: blastn -query GCF_012274265.1_ASM1227426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg552e5a7d-8101-4dd3-afd4-49bc3a09cbde/dqc_reference/reference_markers.fasta -out GCF_012274265.1_ASM1227426v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:30,576] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:30,581] [INFO] Selected 16 target genomes.
[2024-01-24 10:47:30,581] [INFO] Target genome list was writen to GCF_012274265.1_ASM1227426v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:38,472] [INFO] Task started: fastANI
[2024-01-24 10:47:38,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb593d22-6af8-405a-8175-8e12d279b528/GCF_012274265.1_ASM1227426v1_genomic.fna.gz --refList GCF_012274265.1_ASM1227426v1_genomic.fna/target_genomes.txt --output GCF_012274265.1_ASM1227426v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:53,501] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:53,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg552e5a7d-8101-4dd3-afd4-49bc3a09cbde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:53,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg552e5a7d-8101-4dd3-afd4-49bc3a09cbde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:53,515] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:53,515] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:53,516] [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 microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	100.0	1148	1149	95	conclusive
Sphingopyxis bauzanensis	strain=DSM 22271	GCA_002205675.1	651663	651663	type	True	87.0148	874	1149	95	below_threshold
Sphingopyxis bauzanensis	strain=CGMCC 1.8959	GCA_014645635.1	651663	651663	type	True	86.9791	872	1149	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	86.8592	837	1149	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	85.4968	849	1149	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	85.3179	865	1149	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	84.8118	791	1149	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	84.6669	832	1149	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	84.4676	840	1149	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	84.2426	755	1149	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	83.4509	784	1149	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.3333	332	1149	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.2759	371	1149	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.2121	344	1149	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.7553	265	1149	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	77.6063	240	1149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:53,517] [INFO] DFAST Taxonomy check result was written to GCF_012274265.1_ASM1227426v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:53,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:53,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:53,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg552e5a7d-8101-4dd3-afd4-49bc3a09cbde/dqc_reference/checkm_data
[2024-01-24 10:47:53,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:53,558] [INFO] Task started: CheckM
[2024-01-24 10:47:53,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012274265.1_ASM1227426v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012274265.1_ASM1227426v1_genomic.fna/checkm_input GCF_012274265.1_ASM1227426v1_genomic.fna/checkm_result
[2024-01-24 10:48:26,313] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:26,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:26,333] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:26,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:26,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012274265.1_ASM1227426v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:26,334] [INFO] Task started: Blastn
[2024-01-24 10:48:26,334] [INFO] Running command: blastn -query GCF_012274265.1_ASM1227426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg552e5a7d-8101-4dd3-afd4-49bc3a09cbde/dqc_reference/reference_markers_gtdb.fasta -out GCF_012274265.1_ASM1227426v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:28,142] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:28,146] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:28,147] [INFO] Target genome list was writen to GCF_012274265.1_ASM1227426v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:28,187] [INFO] Task started: fastANI
[2024-01-24 10:48:28,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb593d22-6af8-405a-8175-8e12d279b528/GCF_012274265.1_ASM1227426v1_genomic.fna.gz --refList GCF_012274265.1_ASM1227426v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012274265.1_ASM1227426v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:45,957] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:45,977] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:45,977] [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_012274265.1	s__Sphingopyxis microcysteis	100.0	1148	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.26	96.26	0.86	0.86	2	conclusive
GCF_005503695.1	s__Sphingopyxis sp003609815	94.9635	968	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.15	97.15	0.90	0.90	2	-
GCA_002454115.1	s__Sphingopyxis sp002454115	87.4754	891	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.96	0.96	2	-
GCF_005502465.1	s__Sphingopyxis sp005502465	87.4535	900	1149	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	87.4034	869	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205675.1	s__Sphingopyxis bauzanensis	87.0148	874	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015475875.1	s__Sphingopyxis solisilvae	86.8592	837	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.45	96.45	0.86	0.86	2	-
GCF_000756375.1	s__Sphingopyxis sp000756375	85.8112	857	1149	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	85.717	879	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.20	99.20	0.88	0.88	2	-
GCA_900078365.1	s__Sphingopyxis sp900078365	85.5087	858	1149	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	85.4968	849	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756385.1	s__Sphingopyxis sp000756385	85.4169	839	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410105.1	s__Sphingopyxis sp013410105	85.1547	851	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
GCF_900108295.1	s__Sphingopyxis sp900108295	84.865	850	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745175.1	s__Sphingopyxis sp017745175	84.6268	811	1149	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	84.5902	737	1149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001047015.1	s__Sphingopyxis sp001047015	84.5148	867	1149	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 10:48:45,979] [INFO] GTDB search result was written to GCF_012274265.1_ASM1227426v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:45,980] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:45,987] [INFO] DFAST_QC result json was written to GCF_012274265.1_ASM1227426v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:45,988] [INFO] DFAST_QC completed!
[2024-01-24 10:48:45,988] [INFO] Total running time: 0h1m34s