[2024-01-24 14:55:08,662] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg75c1063b-3d33-4c69-b1e8-ab039e523e95/dqc_reference
[2024-01-24 14:55:10,189] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:10,190] [INFO] Task started: Prodigal
[2024-01-24 14:55:10,190] [INFO] Running command: gunzip -c /var/lib/cwl/stgda053ac6-4b45-46dd-9ebf-23b5d5621804/GCF_030284385.1_ASM3028438v1_genomic.fna.gz | prodigal -d GCF_030284385.1_ASM3028438v1_genomic.fna/cds.fna -a GCF_030284385.1_ASM3028438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:17,512] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:17,512] [INFO] Task started: HMMsearch
[2024-01-24 14:55:17,513] [INFO] Running command: hmmsearch --tblout GCF_030284385.1_ASM3028438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75c1063b-3d33-4c69-b1e8-ab039e523e95/dqc_reference/reference_markers.hmm GCF_030284385.1_ASM3028438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:17,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:17,768] [INFO] Found 6/6 markers.
[2024-01-24 14:55:17,794] [INFO] Query marker FASTA was written to GCF_030284385.1_ASM3028438v1_genomic.fna/markers.fasta
[2024-01-24 14:55:17,794] [INFO] Task started: Blastn
[2024-01-24 14:55:17,794] [INFO] Running command: blastn -query GCF_030284385.1_ASM3028438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75c1063b-3d33-4c69-b1e8-ab039e523e95/dqc_reference/reference_markers.fasta -out GCF_030284385.1_ASM3028438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:18,482] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:18,485] [INFO] Selected 27 target genomes.
[2024-01-24 14:55:18,485] [INFO] Target genome list was writen to GCF_030284385.1_ASM3028438v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:18,513] [INFO] Task started: fastANI
[2024-01-24 14:55:18,513] [INFO] Running command: fastANI --query /var/lib/cwl/stgda053ac6-4b45-46dd-9ebf-23b5d5621804/GCF_030284385.1_ASM3028438v1_genomic.fna.gz --refList GCF_030284385.1_ASM3028438v1_genomic.fna/target_genomes.txt --output GCF_030284385.1_ASM3028438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:32,385] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:32,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75c1063b-3d33-4c69-b1e8-ab039e523e95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:32,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75c1063b-3d33-4c69-b1e8-ab039e523e95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:32,405] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:32,405] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:55:32,406] [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
Altererythrobacter ishigakiensis	strain=ATCC BAA-2084	GCA_007830695.1	476157	476157	type	True	81.8007	512	765	95	below_threshold
Altererythrobacter ishigakiensis	strain=NBRC 107699	GCA_001663155.1	476157	476157	type	True	81.7026	518	765	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	78.4852	275	765	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	78.2393	212	765	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.1307	214	765	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	78.0848	99	765	95	below_threshold
Parerythrobacter jejuensis	strain=JCM 16677	GCA_009827995.1	795812	795812	type	True	78.0135	229	765	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.9775	245	765	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.9691	215	765	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	77.812	203	765	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	77.7441	216	765	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.7434	213	765	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	77.7185	193	765	95	below_threshold
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	77.6695	218	765	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	77.6669	218	765	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	77.6607	189	765	95	below_threshold
Erythrobacter insulae	strain=JBTF-M21	GCA_007004095.1	2584124	2584124	type	True	77.5585	212	765	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.5043	158	765	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.4985	196	765	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	77.4332	214	765	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	77.3591	165	765	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	77.3503	240	765	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	77.2345	183	765	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	77.0427	100	765	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	76.9681	130	765	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	76.7899	98	765	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	76.6644	106	765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:32,407] [INFO] DFAST Taxonomy check result was written to GCF_030284385.1_ASM3028438v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:32,408] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:32,408] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:32,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75c1063b-3d33-4c69-b1e8-ab039e523e95/dqc_reference/checkm_data
[2024-01-24 14:55:32,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:32,435] [INFO] Task started: CheckM
[2024-01-24 14:55:32,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030284385.1_ASM3028438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030284385.1_ASM3028438v1_genomic.fna/checkm_input GCF_030284385.1_ASM3028438v1_genomic.fna/checkm_result
[2024-01-24 14:56:00,562] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:00,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:00,580] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:00,580] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:00,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030284385.1_ASM3028438v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:00,581] [INFO] Task started: Blastn
[2024-01-24 14:56:00,581] [INFO] Running command: blastn -query GCF_030284385.1_ASM3028438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75c1063b-3d33-4c69-b1e8-ab039e523e95/dqc_reference/reference_markers_gtdb.fasta -out GCF_030284385.1_ASM3028438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:01,550] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:01,565] [INFO] Selected 15 target genomes.
[2024-01-24 14:56:01,566] [INFO] Target genome list was writen to GCF_030284385.1_ASM3028438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:01,613] [INFO] Task started: fastANI
[2024-01-24 14:56:01,614] [INFO] Running command: fastANI --query /var/lib/cwl/stgda053ac6-4b45-46dd-9ebf-23b5d5621804/GCF_030284385.1_ASM3028438v1_genomic.fna.gz --refList GCF_030284385.1_ASM3028438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030284385.1_ASM3028438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:10,280] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:10,296] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:10,296] [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
GCA_003149575.1	s__Erythrobacter sp003149575	99.2344	733	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	98.16	98.16	0.93	0.93	2	conclusive
GCA_013002295.1	s__Erythrobacter sp013002295	87.1408	491	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.14	98.90	0.85	0.82	4	-
GCF_001663155.1	s__Erythrobacter ishigakiensis	81.6885	519	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	97.03	96.25	0.95	0.94	6	-
GCF_011047315.1	s__Erythrobacter sp011047315	79.2077	376	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013371495.1	s__Erythrobacter sp013371495	78.4852	275	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001515985.1	s__Erythrobacter sp001515985	78.3546	270	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	78.2671	298	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	77.7672	253	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	77.755	179	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	77.7186	193	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001296025.1	s__Erythrobacter sp001296025	77.673	235	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434975.1	s__Parerythrobacter lutipelagi	77.6331	230	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724215.1	s__Erythrobacter sp001724215	77.5408	200	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524425.1	s__Erythrobacter sp011524425	77.4002	142	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542875.1	s__Erythrobacter sp001542875	77.3964	184	765	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:10,299] [INFO] GTDB search result was written to GCF_030284385.1_ASM3028438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:10,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:10,303] [INFO] DFAST_QC result json was written to GCF_030284385.1_ASM3028438v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:10,303] [INFO] DFAST_QC completed!
[2024-01-24 14:56:10,303] [INFO] Total running time: 0h1m2s