[2023-06-04 22:42:04,594] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:42:04,599] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:42:04,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d9ba8ed-5b88-4b17-b231-8ceccbfffc6b/dqc_reference
[2023-06-04 22:42:06,885] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:42:06,886] [INFO] Task started: Prodigal
[2023-06-04 22:42:06,886] [INFO] Running command: gunzip -c /var/lib/cwl/stge45ffa75-9e66-4020-aee3-fc60406a72fe/GCA_004282995.1_ASM428299v1_genomic.fna.gz | prodigal -d GCA_004282995.1_ASM428299v1_genomic.fna/cds.fna -a GCA_004282995.1_ASM428299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:42:12,091] [INFO] Task succeeded: Prodigal
[2023-06-04 22:42:12,092] [INFO] Task started: HMMsearch
[2023-06-04 22:42:12,092] [INFO] Running command: hmmsearch --tblout GCA_004282995.1_ASM428299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d9ba8ed-5b88-4b17-b231-8ceccbfffc6b/dqc_reference/reference_markers.hmm GCA_004282995.1_ASM428299v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:42:12,310] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:42:12,312] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge45ffa75-9e66-4020-aee3-fc60406a72fe/GCA_004282995.1_ASM428299v1_genomic.fna.gz]
[2023-06-04 22:42:12,337] [INFO] Query marker FASTA was written to GCA_004282995.1_ASM428299v1_genomic.fna/markers.fasta
[2023-06-04 22:42:12,338] [INFO] Task started: Blastn
[2023-06-04 22:42:12,338] [INFO] Running command: blastn -query GCA_004282995.1_ASM428299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d9ba8ed-5b88-4b17-b231-8ceccbfffc6b/dqc_reference/reference_markers.fasta -out GCA_004282995.1_ASM428299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:42:13,059] [INFO] Task succeeded: Blastn
[2023-06-04 22:42:13,064] [INFO] Selected 22 target genomes.
[2023-06-04 22:42:13,064] [INFO] Target genome list was writen to GCA_004282995.1_ASM428299v1_genomic.fna/target_genomes.txt
[2023-06-04 22:42:13,096] [INFO] Task started: fastANI
[2023-06-04 22:42:13,096] [INFO] Running command: fastANI --query /var/lib/cwl/stge45ffa75-9e66-4020-aee3-fc60406a72fe/GCA_004282995.1_ASM428299v1_genomic.fna.gz --refList GCA_004282995.1_ASM428299v1_genomic.fna/target_genomes.txt --output GCA_004282995.1_ASM428299v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:42:23,809] [INFO] Task succeeded: fastANI
[2023-06-04 22:42:23,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d9ba8ed-5b88-4b17-b231-8ceccbfffc6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:42:23,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d9ba8ed-5b88-4b17-b231-8ceccbfffc6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:42:23,832] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:42:23,832] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 22:42:23,832] [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
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.5812	238	554	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.4003	243	554	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.299	264	554	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	78.2414	221	554	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.1962	216	554	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	78.1749	208	554	95	below_threshold
Parerythrobacter jejuensis	strain=JCM 16677	GCA_009827995.1	795812	795812	type	True	78.1036	277	554	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	78.0812	214	554	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.0031	224	554	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	77.9963	223	554	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.9616	204	554	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	77.9286	187	554	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	77.8756	181	554	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.8674	201	554	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	77.8636	199	554	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.8263	199	554	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.7585	213	554	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	77.7207	180	554	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.6652	213	554	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	77.5741	142	554	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	77.4205	195	554	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	76.8004	133	554	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 22:42:23,835] [INFO] DFAST Taxonomy check result was written to GCA_004282995.1_ASM428299v1_genomic.fna/tc_result.tsv
[2023-06-04 22:42:23,835] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:42:23,835] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:42:23,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d9ba8ed-5b88-4b17-b231-8ceccbfffc6b/dqc_reference/checkm_data
[2023-06-04 22:42:23,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:42:23,863] [INFO] Task started: CheckM
[2023-06-04 22:42:23,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004282995.1_ASM428299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004282995.1_ASM428299v1_genomic.fna/checkm_input GCA_004282995.1_ASM428299v1_genomic.fna/checkm_result
[2023-06-04 22:42:45,192] [INFO] Task succeeded: CheckM
[2023-06-04 22:42:45,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:42:45,215] [INFO] ===== Completeness check finished =====
[2023-06-04 22:42:45,215] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:42:45,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004282995.1_ASM428299v1_genomic.fna/markers.fasta)
[2023-06-04 22:42:45,216] [INFO] Task started: Blastn
[2023-06-04 22:42:45,216] [INFO] Running command: blastn -query GCA_004282995.1_ASM428299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d9ba8ed-5b88-4b17-b231-8ceccbfffc6b/dqc_reference/reference_markers_gtdb.fasta -out GCA_004282995.1_ASM428299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:42:46,371] [INFO] Task succeeded: Blastn
[2023-06-04 22:42:46,377] [INFO] Selected 17 target genomes.
[2023-06-04 22:42:46,377] [INFO] Target genome list was writen to GCA_004282995.1_ASM428299v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:42:46,526] [INFO] Task started: fastANI
[2023-06-04 22:42:46,526] [INFO] Running command: fastANI --query /var/lib/cwl/stge45ffa75-9e66-4020-aee3-fc60406a72fe/GCA_004282995.1_ASM428299v1_genomic.fna.gz --refList GCA_004282995.1_ASM428299v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004282995.1_ASM428299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:42:54,870] [INFO] Task succeeded: fastANI
[2023-06-04 22:42:54,884] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:42:54,884] [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_004282995.1	s__Altererythrobacter_D sp004282995	100.0	547	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_D	95.0	99.06	99.06	0.84	0.84	2	conclusive
GCF_000013005.1	s__Altererythrobacter_D litoralis_A	79.9692	338	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.594	277	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018205975.1	s__Erythrobacter sp018205975	78.423	246	554	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	78.2474	254	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248395.1	s__Qipengyuania sp003248395	78.0862	173	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	78.0839	209	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	78.0031	224	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	77.9329	225	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	77.8673	207	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	77.8504	229	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCA_001515985.1	s__Erythrobacter sp001515985	77.7915	169	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269345.1	s__Tsuneonella mangrovi	77.7715	178	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	77.7634	177	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	77.7595	177	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125555.1	s__Erythrobacter sp016125555	77.6563	229	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	77.5192	130	554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 22:42:54,886] [INFO] GTDB search result was written to GCA_004282995.1_ASM428299v1_genomic.fna/result_gtdb.tsv
[2023-06-04 22:42:54,887] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:42:54,895] [INFO] DFAST_QC result json was written to GCA_004282995.1_ASM428299v1_genomic.fna/dqc_result.json
[2023-06-04 22:42:54,896] [INFO] DFAST_QC completed!
[2023-06-04 22:42:54,896] [INFO] Total running time: 0h0m50s