[2024-01-24 11:48:21,289] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,290] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,290] [INFO] DQC Reference Directory: /var/lib/cwl/stgba749496-8f71-413a-b014-c77ac011f360/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,565] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,566] [INFO] Running command: gunzip -c /var/lib/cwl/stg5605c435-48b6-4d9a-8ee8-c3d9384f1447/GCF_014645635.1_ASM1464563v1_genomic.fna.gz | prodigal -d GCF_014645635.1_ASM1464563v1_genomic.fna/cds.fna -a GCF_014645635.1_ASM1464563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:36,851] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:36,851] [INFO] Task started: HMMsearch
[2024-01-24 11:48:36,851] [INFO] Running command: hmmsearch --tblout GCF_014645635.1_ASM1464563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba749496-8f71-413a-b014-c77ac011f360/dqc_reference/reference_markers.hmm GCF_014645635.1_ASM1464563v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:37,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:37,144] [INFO] Found 6/6 markers.
[2024-01-24 11:48:37,182] [INFO] Query marker FASTA was written to GCF_014645635.1_ASM1464563v1_genomic.fna/markers.fasta
[2024-01-24 11:48:37,182] [INFO] Task started: Blastn
[2024-01-24 11:48:37,182] [INFO] Running command: blastn -query GCF_014645635.1_ASM1464563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba749496-8f71-413a-b014-c77ac011f360/dqc_reference/reference_markers.fasta -out GCF_014645635.1_ASM1464563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:38,082] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:38,086] [INFO] Selected 14 target genomes.
[2024-01-24 11:48:38,086] [INFO] Target genome list was writen to GCF_014645635.1_ASM1464563v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:38,094] [INFO] Task started: fastANI
[2024-01-24 11:48:38,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg5605c435-48b6-4d9a-8ee8-c3d9384f1447/GCF_014645635.1_ASM1464563v1_genomic.fna.gz --refList GCF_014645635.1_ASM1464563v1_genomic.fna/target_genomes.txt --output GCF_014645635.1_ASM1464563v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:48:49,851] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:49,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba749496-8f71-413a-b014-c77ac011f360/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:48:49,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba749496-8f71-413a-b014-c77ac011f360/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:48:49,863] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:48:49,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:48:49,863] [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 bauzanensis	strain=CGMCC 1.8959	GCA_014645635.1	651663	651663	type	True	100.0	1384	1386	95	conclusive
Sphingopyxis bauzanensis	strain=DSM 22271	GCA_002205675.1	651663	651663	type	True	99.9896	1381	1386	95	conclusive
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	87.1951	843	1386	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	86.2663	856	1386	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	84.9836	895	1386	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	84.8633	865	1386	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	84.0229	782	1386	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	84.0127	775	1386	95	below_threshold
Sphingopyxis witflariensis	strain=DSM 14551	GCA_002205635.1	173675	173675	type	True	83.5906	828	1386	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.8792	341	1386	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.627	328	1386	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.6064	251	1386	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.5299	334	1386	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.3306	193	1386	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:48:49,865] [INFO] DFAST Taxonomy check result was written to GCF_014645635.1_ASM1464563v1_genomic.fna/tc_result.tsv
[2024-01-24 11:48:49,865] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:48:49,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:48:49,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba749496-8f71-413a-b014-c77ac011f360/dqc_reference/checkm_data
[2024-01-24 11:48:49,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:48:49,905] [INFO] Task started: CheckM
[2024-01-24 11:48:49,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645635.1_ASM1464563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645635.1_ASM1464563v1_genomic.fna/checkm_input GCF_014645635.1_ASM1464563v1_genomic.fna/checkm_result
[2024-01-24 11:49:27,463] [INFO] Task succeeded: CheckM
[2024-01-24 11:49:27,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:49:27,480] [INFO] ===== Completeness check finished =====
[2024-01-24 11:49:27,480] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:49:27,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645635.1_ASM1464563v1_genomic.fna/markers.fasta)
[2024-01-24 11:49:27,481] [INFO] Task started: Blastn
[2024-01-24 11:49:27,481] [INFO] Running command: blastn -query GCF_014645635.1_ASM1464563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba749496-8f71-413a-b014-c77ac011f360/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645635.1_ASM1464563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:49:29,121] [INFO] Task succeeded: Blastn
[2024-01-24 11:49:29,124] [INFO] Selected 11 target genomes.
[2024-01-24 11:49:29,125] [INFO] Target genome list was writen to GCF_014645635.1_ASM1464563v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:49:29,141] [INFO] Task started: fastANI
[2024-01-24 11:49:29,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg5605c435-48b6-4d9a-8ee8-c3d9384f1447/GCF_014645635.1_ASM1464563v1_genomic.fna.gz --refList GCF_014645635.1_ASM1464563v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645635.1_ASM1464563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:49:40,734] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:40,750] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:49:40,751] [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_002205675.1	s__Sphingopyxis bauzanensis	99.9896	1381	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_018823905.1	s__Sphingopyxis sp018823905	89.7166	807	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.80	99.78	0.95	0.94	3	-
GCA_002454115.1	s__Sphingopyxis sp002454115	88.9467	883	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.96	0.96	2	-
GCA_016463225.1	s__Sphingopyxis sp016463225	88.4948	859	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502465.1	s__Sphingopyxis sp005502465	88.2219	900	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704835.1	s__Sphingopyxis sp016704835	87.7114	894	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012274265.1	s__Sphingopyxis microcysteis	87.1803	844	1386	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	87.1108	873	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.15	97.15	0.90	0.90	2	-
GCF_015475875.1	s__Sphingopyxis solisilvae	86.2661	856	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.45	96.45	0.86	0.86	2	-
GCF_000803645.1	s__Sphingopyxis fribergensis	84.9766	896	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108295.1	s__Sphingopyxis sp900108295	83.7549	830	1386	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 11:49:40,752] [INFO] GTDB search result was written to GCF_014645635.1_ASM1464563v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:49:40,752] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:49:40,756] [INFO] DFAST_QC result json was written to GCF_014645635.1_ASM1464563v1_genomic.fna/dqc_result.json
[2024-01-24 11:49:40,756] [INFO] DFAST_QC completed!
[2024-01-24 11:49:40,756] [INFO] Total running time: 0h1m19s