[2024-01-25 19:58:20,578] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:20,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:20,579] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd1ddb8f-67f5-4843-9f6b-8a533d3137f3/dqc_reference
[2024-01-25 19:58:21,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:21,720] [INFO] Task started: Prodigal
[2024-01-25 19:58:21,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ff8b3d6-1855-4829-84c5-52f9f7662f50/GCF_003340475.1_ASM334047v1_genomic.fna.gz | prodigal -d GCF_003340475.1_ASM334047v1_genomic.fna/cds.fna -a GCF_003340475.1_ASM334047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:29,328] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:29,329] [INFO] Task started: HMMsearch
[2024-01-25 19:58:29,329] [INFO] Running command: hmmsearch --tblout GCF_003340475.1_ASM334047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd1ddb8f-67f5-4843-9f6b-8a533d3137f3/dqc_reference/reference_markers.hmm GCF_003340475.1_ASM334047v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:29,522] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:29,523] [INFO] Found 6/6 markers.
[2024-01-25 19:58:29,551] [INFO] Query marker FASTA was written to GCF_003340475.1_ASM334047v1_genomic.fna/markers.fasta
[2024-01-25 19:58:29,551] [INFO] Task started: Blastn
[2024-01-25 19:58:29,551] [INFO] Running command: blastn -query GCF_003340475.1_ASM334047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd1ddb8f-67f5-4843-9f6b-8a533d3137f3/dqc_reference/reference_markers.fasta -out GCF_003340475.1_ASM334047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:30,314] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:30,316] [INFO] Selected 25 target genomes.
[2024-01-25 19:58:30,317] [INFO] Target genome list was writen to GCF_003340475.1_ASM334047v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:30,335] [INFO] Task started: fastANI
[2024-01-25 19:58:30,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ff8b3d6-1855-4829-84c5-52f9f7662f50/GCF_003340475.1_ASM334047v1_genomic.fna.gz --refList GCF_003340475.1_ASM334047v1_genomic.fna/target_genomes.txt --output GCF_003340475.1_ASM334047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:42,915] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:42,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd1ddb8f-67f5-4843-9f6b-8a533d3137f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:42,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd1ddb8f-67f5-4843-9f6b-8a533d3137f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:42,930] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:58:42,930] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:42,930] [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
Alteripontixanthobacter maritimus	strain=HME9302	GCA_003340475.1	2161824	2161824	type	True	100.0	887	892	95	conclusive
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.1472	233	892	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.115	340	892	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.9631	297	892	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	77.9253	319	892	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	77.9066	280	892	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	77.9066	257	892	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	77.8908	244	892	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	77.8895	282	892	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.8824	294	892	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	77.869	225	892	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	77.8271	245	892	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.8218	225	892	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.7934	250	892	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	77.7594	306	892	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	77.7322	247	892	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.7214	275	892	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	77.6627	257	892	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.6403	275	892	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	77.6248	218	892	95	below_threshold
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	77.6133	269	892	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	77.5774	215	892	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.5521	266	892	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	77.4931	275	892	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	77.4884	269	892	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:42,932] [INFO] DFAST Taxonomy check result was written to GCF_003340475.1_ASM334047v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:42,932] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:42,932] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:42,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd1ddb8f-67f5-4843-9f6b-8a533d3137f3/dqc_reference/checkm_data
[2024-01-25 19:58:42,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:42,963] [INFO] Task started: CheckM
[2024-01-25 19:58:42,963] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003340475.1_ASM334047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003340475.1_ASM334047v1_genomic.fna/checkm_input GCF_003340475.1_ASM334047v1_genomic.fna/checkm_result
[2024-01-25 19:59:08,717] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:08,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:08,753] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:08,754] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:08,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003340475.1_ASM334047v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:08,754] [INFO] Task started: Blastn
[2024-01-25 19:59:08,754] [INFO] Running command: blastn -query GCF_003340475.1_ASM334047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd1ddb8f-67f5-4843-9f6b-8a533d3137f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003340475.1_ASM334047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:10,210] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:10,213] [INFO] Selected 25 target genomes.
[2024-01-25 19:59:10,213] [INFO] Target genome list was writen to GCF_003340475.1_ASM334047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:10,264] [INFO] Task started: fastANI
[2024-01-25 19:59:10,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ff8b3d6-1855-4829-84c5-52f9f7662f50/GCF_003340475.1_ASM334047v1_genomic.fna.gz --refList GCF_003340475.1_ASM334047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003340475.1_ASM334047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:24,511] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:24,525] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:59:24,526] [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_003340475.1	s__Alteripontixanthobacter maritimus	100.0	885	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteripontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.1771	297	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	78.1116	341	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	78.0805	322	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.0424	291	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	78.0326	306	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828015.1	s__Qipengyuania citrea	77.9523	307	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCF_009827515.1	s__Pelagerythrobacter marinus	77.9253	319	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	77.9189	304	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	77.9066	257	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605195.1	s__Alteraurantiacibacter odishensis	77.8908	244	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	77.8218	225	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	77.808	283	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCF_001677335.1	s__Erythrobacter dokdonensis	77.7934	250	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013370205.1	s__Actirhodobacter atriluteus	77.7411	244	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Actirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	77.6741	256	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767595.1	s__Qipengyuania sp002895025	77.6411	207	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_009827615.1	s__Pseudopontixanthobacter_A confluentis	77.625	268	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827305.1	s__Croceibacterium xixiisoli	77.5559	225	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	77.5403	267	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605755.1	s__Tsuneonella suprasediminis	77.5238	221	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	77.4747	208	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002870965.1	s__Tsuneonella flava	77.441	235	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	99.01	98.03	0.92	0.87	3	-
GCA_002337385.1	s__Alteraurantiacibacter sp002337385	77.3848	183	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827395.1	s__Pontixanthobacter aquaemixtae	77.2748	225	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:24,527] [INFO] GTDB search result was written to GCF_003340475.1_ASM334047v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:24,527] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:24,531] [INFO] DFAST_QC result json was written to GCF_003340475.1_ASM334047v1_genomic.fna/dqc_result.json
[2024-01-25 19:59:24,531] [INFO] DFAST_QC completed!
[2024-01-25 19:59:24,531] [INFO] Total running time: 0h1m4s