[2024-01-24 13:13:37,288] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:37,290] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:37,290] [INFO] DQC Reference Directory: /var/lib/cwl/stge6e3821d-fd1a-437b-882f-bb29ee3f43ac/dqc_reference
[2024-01-24 13:13:38,547] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:38,549] [INFO] Task started: Prodigal
[2024-01-24 13:13:38,550] [INFO] Running command: gunzip -c /var/lib/cwl/stga5ab6ac1-7918-47d5-a3ee-92ee3859cb19/GCF_009827595.1_ASM982759v1_genomic.fna.gz | prodigal -d GCF_009827595.1_ASM982759v1_genomic.fna/cds.fna -a GCF_009827595.1_ASM982759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:49,978] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:49,979] [INFO] Task started: HMMsearch
[2024-01-24 13:13:49,979] [INFO] Running command: hmmsearch --tblout GCF_009827595.1_ASM982759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6e3821d-fd1a-437b-882f-bb29ee3f43ac/dqc_reference/reference_markers.hmm GCF_009827595.1_ASM982759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:50,218] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:50,219] [INFO] Found 6/6 markers.
[2024-01-24 13:13:50,253] [INFO] Query marker FASTA was written to GCF_009827595.1_ASM982759v1_genomic.fna/markers.fasta
[2024-01-24 13:13:50,253] [INFO] Task started: Blastn
[2024-01-24 13:13:50,253] [INFO] Running command: blastn -query GCF_009827595.1_ASM982759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6e3821d-fd1a-437b-882f-bb29ee3f43ac/dqc_reference/reference_markers.fasta -out GCF_009827595.1_ASM982759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:51,043] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:51,047] [INFO] Selected 22 target genomes.
[2024-01-24 13:13:51,047] [INFO] Target genome list was writen to GCF_009827595.1_ASM982759v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:51,056] [INFO] Task started: fastANI
[2024-01-24 13:13:51,056] [INFO] Running command: fastANI --query /var/lib/cwl/stga5ab6ac1-7918-47d5-a3ee-92ee3859cb19/GCF_009827595.1_ASM982759v1_genomic.fna.gz --refList GCF_009827595.1_ASM982759v1_genomic.fna/target_genomes.txt --output GCF_009827595.1_ASM982759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:03,822] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:03,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6e3821d-fd1a-437b-882f-bb29ee3f43ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:03,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6e3821d-fd1a-437b-882f-bb29ee3f43ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:03,840] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:03,840] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:03,840] [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
Altericroceibacterium endophyticum	strain=LMG 29518	GCA_009827595.1	1808508	1808508	type	True	100.0	1151	1151	95	conclusive
Altericroceibacterium indicum	strain=DSM 18604	GCA_009828105.1	374177	374177	type	True	78.8331	328	1151	95	below_threshold
Altericroceibacterium spongiae	strain=HN-Y73	GCA_003610805.1	2320269	2320269	type	True	78.5548	352	1151	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	78.4571	351	1151	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	78.4294	353	1151	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	77.6862	198	1151	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	77.6461	200	1151	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.5808	168	1151	95	below_threshold
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	77.544	224	1151	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	77.5315	249	1151	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	77.4464	178	1151	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	77.3561	192	1151	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.3163	158	1151	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	77.3076	213	1151	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	77.2593	165	1151	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	77.202	184	1151	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	77.1628	192	1151	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	77.1523	190	1151	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	76.9492	156	1151	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	76.8712	141	1151	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	76.6224	136	1151	95	below_threshold
Sphingorhabdus contaminans	strain=KCTC32445	GCA_007280415.1	1343899	1343899	type	True	76.6066	85	1151	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,842] [INFO] DFAST Taxonomy check result was written to GCF_009827595.1_ASM982759v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:03,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:03,843] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:03,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6e3821d-fd1a-437b-882f-bb29ee3f43ac/dqc_reference/checkm_data
[2024-01-24 13:14:03,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:03,880] [INFO] Task started: CheckM
[2024-01-24 13:14:03,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827595.1_ASM982759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827595.1_ASM982759v1_genomic.fna/checkm_input GCF_009827595.1_ASM982759v1_genomic.fna/checkm_result
[2024-01-24 13:14:38,665] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:38,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:38,695] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:38,695] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:38,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827595.1_ASM982759v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:38,696] [INFO] Task started: Blastn
[2024-01-24 13:14:38,696] [INFO] Running command: blastn -query GCF_009827595.1_ASM982759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6e3821d-fd1a-437b-882f-bb29ee3f43ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827595.1_ASM982759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:40,029] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:40,038] [INFO] Selected 23 target genomes.
[2024-01-24 13:14:40,038] [INFO] Target genome list was writen to GCF_009827595.1_ASM982759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:40,083] [INFO] Task started: fastANI
[2024-01-24 13:14:40,083] [INFO] Running command: fastANI --query /var/lib/cwl/stga5ab6ac1-7918-47d5-a3ee-92ee3859cb19/GCF_009827595.1_ASM982759v1_genomic.fna.gz --refList GCF_009827595.1_ASM982759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827595.1_ASM982759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:53,523] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:53,541] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:53,542] [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_009827595.1	s__Altericroceibacterium endophyticum	100.0	1151	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009828105.1	s__Altericroceibacterium indicum	78.8282	329	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610805.1	s__Altericroceibacterium spongiae	78.5548	352	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	78.4294	353	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001305965.1	s__Caenibius sp001305965	77.9071	298	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	77.7529	295	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	77.7196	201	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014983025.1	s__Erythrobacter sp014983025	77.6901	188	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	77.6862	198	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004114695.1	s__Parerythrobacter sp004114695	77.5646	177	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	77.5399	267	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012979275.1	s__Pseudopontixanthobacter vadosimaris	77.4993	195	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958635.1	s__Altericroceibacterium_A xinjiangense	77.4672	200	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625325.1	s__Caenibius estronivorus	77.3964	176	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003149575.1	s__Erythrobacter sp003149575	77.2893	131	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	98.16	98.16	0.93	0.93	2	-
GCF_009827515.1	s__Pelagerythrobacter marinus	77.1628	192	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744735.1	s__Caenibius sp017744735	77.1078	195	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCF_013149295.1	s__Novosphingobium sp013149295	76.9915	199	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744315.1	s__Croceibacterium sp017744315	76.9467	182	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	76.9423	176	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367345.1	s__Sphingobium xenophagum	76.8889	141	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.29	96.67	0.79	0.71	22	-
GCF_014280435.1	s__Sphingobium sp014280435	76.8604	137	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463275.1	s__Sphingobium sp016463275	76.192	100	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:53,543] [INFO] GTDB search result was written to GCF_009827595.1_ASM982759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:53,544] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:53,549] [INFO] DFAST_QC result json was written to GCF_009827595.1_ASM982759v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:53,550] [INFO] DFAST_QC completed!
[2024-01-24 13:14:53,550] [INFO] Total running time: 0h1m16s